Even though this is a homebrew spell, I think the question should be able to be answered from the rules and come to an applicable conclusion. That being said, all the normal caveats about homebrew material apply.
I am adhering very strictly to RAW (to the point of being over-strict possibly) due to your DM's ruling policy and your request.
I'm going to assume in my argument that you are only trying to create the actual ink and not also a bottle to hold it in.
Choose one creature or nonmagical object that you can see within
range. You transform the creature into a different creature, the
creature into an object, or the object into a creature [...]
Creature into Object. If you turn a creature into an object, it
transforms along with whatever it is wearing and carrying into that
form. The creature's statistics become those of the object, and the
creature has no memory of time spent in this form, after the spell
ends and it returns to its normal form. (basic rules)
Definition of object:
[A]n object is a discrete, inanimate item like a window, door, sword, book, table, chair, or stone, not a building or a vehicle that is composed of many other objects. (Basic Rules)
Note on this definition
D&D5e likely specifically left this definition vague so that DMs could and should decide for themselves what is an object and what is not. Thus, this is almost always going to boil down to DM fiat at some point. However, RAW does offer some guidance beyond just that.
Your DM is technically not following RAW by disallowing objects with multiple materials
Objects composed of different materials are still considered one object
The good news here for your argument is that there are things in the definition that are obviously composed of more than one piece or material and still considered a single object (a window for example). A musical instrument, some of which can be very complex, have also been confirmed to be a single object by Jeremy Crawford. Dead bodies are also single objects (more on this later).
So, your DM's current method of counting different types of molecules as different objects really does not hold weight with the rules.
Strict RAW - TP can't create ink because ink is not discrete
Objects must be discrete
However, we run into a problem right away when it says "discrete".
Liquids are, by their very nature, not discrete. Discrete objects can be easily distinguished and separated from other objects. For example, if I put three different colored ice cubes in a bag and shook it up, I could open the bag and still see 3 different ice cubes and point them out. If I put them in a bowl and let them melt and mixed them up there would be no way to separate them. Thus, ink (and liquids in general) are not discrete. And thus, ink would not be a legal target or result of true polymorph.
So, by this very strict reading, making ink via true polymorph would not be allowed.
In some ways this actually makes sense. If you saw a puddle of ink on a desk would you consider it "an object"? Probably we would more describe it IRL as a substance actually. Regardless the rules are what they are.
Possible things to try
You might be able to get around this by creating a bottle of ink, which, as a whole, would be considered discrete. However, would likely run afoul of your DM's interpretation of how you separate objects out.
Some inks can also come in solid form so maybe you could try that as well.
However, there are possible counterexamples/contradictions
Acid, Oil, and Holy Water
Despite the definition above, the rules specifically allow vials of acid, holy water, and oil to be used as improvised weapons.
Acid. As an action, you can splash the contents of this vial onto a
creature within 5 feet of you or throw the vial up to 20 feet,
shattering it on impact...treating the acid as an improvised
weapon. (basic rules)
The improvised weapon is important in this case because an improvised weapon requires an object:
An improvised weapon includes any object you can wield in one or two
hands, such as broken glass, a table leg, a frying pan, a wagon wheel,
or a dead goblin. (basic rules)
A bottle of acid and ink (or a bottle of ink) are similar enough to say that if one can be considered an object, so can the other.
Also of note is that dead bodies (!) are considered to be objects by the rules. And bodies are composed of many different and varied materials and a LOT of fluid. This creates the interesting ruling that if you hold to strict RAW, any spell you cast on a dead body would not affect the blood, bile, urine, etc. inside the body. This makes no sense and it is not clear what would happen to the body and/or the fluids in the case of a spell affecting the body.
So, if a dead body (composed of lots of materials, essentially just a sack holding a bunch of liquid) can be considered an object it might not be unreasonable to say that ink could be as well (or even a bottle of ink).
If you are going by strict RAW, your answer might just be "no" unless you can convince the DM that these counterexamples make a compelling case for the game intending this to be allowed.
It is possible that your DM has other motives
If your DM created this spell and has a specific spell component in mind, maybe he is using this as some sort of plot hook or interaction hook on purpose and that is why he is limiting you in this case. Worth checking to make sure you are understanding each other.
Regarding spell components
(I still think this question deserves its own question but I'll make a pass at answering it here)
Obviously, if you follow the strict RAW above, anything liquid or gaseous will not be able to be created because of the "distinct" issue.
You can't create living plants because they are neither creatures nor objects.