By the book, this fight should be Hard.
You can use an online CR calculator by figuring out the damage that the monsters would do if their best 3 attacks all hit. You can also use an online encounter builder to see how the xp of your encounter stacks up. Just pick official monsters with the same CRs as your homebrew monsters.
When I put the zombie knight in with 28 hp, 16 ac, 7* avg dmg and +3 attack, the calculator gives a CR of 1/2. * It should probably be using the longsword 2H.
When I put the necromancer in with 25 hp, 14 ac, 13 avg dmg, and +3 attack, the calculator gives a CR of 1/2. Note that the necromancer's strongest attacks are all Magic Missile which always hits, so CR 1 is probably more accurate.
Note that there is a table at MM p8 which shows proficiency bonus vs CR. For CR 0-4, the bonus is +2. You can always bump his stats a little or give him a +1 staff (which can double as a reward) if you want the attack bonus a little higher (although realistically, if this Wizard is using his staff in melee he's already in trouble). Alternatively, maybe his staff (or whatever) gives him an attack bonus so that his firebolt is a little better.
Also note that there are two CR2 NPCs in the MM that you might use to compare against your necromancer: Druid (4th level caster) and Priest (5th level caster).
If you put 4 level 3 PCs into the encounter builder and then add 4 Shadows (CR 1/2) and 1 Ghoul (CR 1) as standins for your homebrews, you get an encounter with 600 xp or 1200 adjusted xp. This is a Hard encounter by the book (900-1600 xp).
Did you get 1000 xp by taking the 4 knights (400 xp) and doubling that (800 xp) and then just adding it to the necromancer (+200 xp) for 1000 xp total? You should add the 400 xp of the knights to the necromancer's 200 xp for 600 xp and then double the whole thing to get 1200 xp. Still hard (this time).
Also note that a 5th level Wizard would have 4 3 2 spell slots and that it only requires a single casting of Animate Dead to maintain control over 4 Undead. So the Necromancer could have 3 3 1 slots left if you want him to (after casting Mage Armor as well). This would bump the damage output of the Boss up a little, but he'd probably still only be CR 1 or CR 2 even after that, so you'd still be in for a Hard(er) fight.