I made it to the end and I have no idea which chest is the right one. I have struggled with this dungeon to get to this point and I am really nervous about making the wrong decision. Does it matter which I even choose or will one do damage to my pet?

It doesn't matter which chest you choose. there are no adverse effects. Just random prizes. Even if you choose the same box each time, the prize will vary.

my pets are level 31 but i am still having trouble defeating the last three bosses in this .. are there any tips?

I can't really tell if you've assigned the level up/proficiency points well, but some of your pet's equipment should be changed. Use equipment that adds more to either strength/intelligence, whichever you chose to add the stat points to. Don't use those that split equally between both/all stats.

I can't remember if there is a pattern to the final boss, so keep an eye on battle log. Always try to kill off the one that deals the most damage first.

Otherwise, go explore in a lower zone just before the boss battle, so you have full health and mana when you start, and use the finishing blows from the start.

Have a good supply of elixirs on hand. Do missions regularly to get a good supply. Use mend whenever your pet drops below 75% health, and change their positions if need be to let one recover a bit more if need be.

I got new equipment, for Bae and Jinx. I have no more gold for elixirs so off to do alot of missions I guess.. thanks.

Yeah, its best if you don't use Disciple and Warden equipment. Hope that helps.