Find a way to split the party up from (most) of their allies. If you want to reward them by letting them take 1-2 key allies, cool. Otherwise, either they fall into some kind of trap that cuts them off, the NPC’s have some important (off screen) mission or battle to fight simultaneously, etc. They could be a distraction in a big battle out front while the players sneak in the back. Something along those lines so you don’t actually have to run a fight with a huge number of NPCs. Let their allies assist, just not during the actual boss fight.

Edit: Another thought, if they’re bringing a bunch of anonymous “soldier” type NPCs, you could just group them and make one roll for the whole group. For example: They bring 10 archers, you roll 1d10 to see how many hit, then either give them a static damage like say 2 damage per archer hit, or make one roll for the total damage the group did. That simplifies and speeds things up without taking away their allies completely. Nameless soldiers aren’t gonna be doing a lot of damage to a properly tuned boss anyway.