Not your choice when compared to other descriptions with the "up to" wording.
Many spells or items have an "up to" in their descriptions and in some of these most people (myself included) assume that the caster may choose to make it less. Two examples are mage hand
You can move the hand up to 30 feet each time you use it.
and a flask of oil:
As an action, you can splash the oil in this flask onto a creature within 5 feet of you or throw it up to 20 feet, shattering it on impact.
I assume we can agree that you may choose in both how far you move the mage hand or throw the bottle.
However note how these spells do not specify that you can choose the direction. Does that mean we cannot choose the direction? Of course we can. It wouldn't really make sense for the direction to be fixed. The flask of oil is here even a better comparison to the catapult spell, because it will also fly in a straight line (unless you can do some cool curve shots). On the other hand the mage hand can move in many directions in one move.
Why is it that these two instances (and others) do not need to specify that one may choose the direction?
The big difference to the catapult spell is, that in these descriptions "you" is the subject of the sentence. This implies that "you" have control over it and can choose the distance and direction.
However in the catapult spell "The object" is the subject of the sentence which implies "you" do not have control over it. That is why it needs the extra clause that "you" can choose the direction.
Ok, but why doesn't the "you choose" part also apply to the distance?
Grammatically you can make a verb refer to two things to avoid repeating it. For example "You choose your colour and group". Here "choose" refers to colour and group. However then when removing one of the things, the sentence still has to make sense with the other (you might have to correct from plural to singular though).
If we leave away the "in a direction" part from the spell description, we get "up to 90 feet you choose before falling to the ground". That does not make any sense. If we were allowed to choose the distance the description would be something like "The object flies in a straight line up to a distance (up to 90 feet) and direction you choose before falling to the ground".
My conclusion is that there is no indication in the description that "you" may choose the distance the object can fly. It will always fly 90 feet unless it hits something.