Looks like the bottom bracket has come apart, there is a ton of play and you can see the bearings. It is square taper so I tried to remove the rear drive side crank arm with a crank puller but it stripped almost all of the threads out while not budging the crank at all. What can I do to resolve this?

Not really anything tandem specific in what you’re doing – even the rear driveside crank isn’t (which makes replacement a lot cheaper).

Very hard to tell without seeing it, but I’d be suspicious that there’s some washer in there you’ve missed – that or you’re using a splined crank extractor. Three standard methods I can think of to remove that. Take it for a ride, doing lots of standing up (but stop as soon as it gets loose). Use a 3 or 4 legged puller. Use a hacksaw / dremel.

Make sure you use a good quality crank puller like a park one. Cheapo ones have shallow threads and pull out easily, taking some of the extractor threads with them.
I managed to rescue a set of cranks using a park one before.

Was the bolt in the puller screwed right out before use ?

A big bar, positioned at the base of the arm at the rear & a smart wack with a good hammer will see it fly off.

to be fair to the OP, if its been on a while and was sparse on the grease originally its entirely possible to strip the threads out of cranks trying to take them off. Usually resort to some sort of fly-wheel puller, requires a bit of finess to get the arms to stay on but should get the arm off. Bit of heat (watch the paint) and a bray with a metal hammer to shock it into loosening will help too.

requires a bit of finess to get the arms to stay on

Zip ties and/or tape helps a lot with this.

Yeah the puller was in all but the very last part of the thread so theres basically none of it left now! I’ll try some of these tips, thanks!