So right now I'm starting off marleybone and I lost my 5 level 48-50 companions in the boss fight after captain kid, and I only have my other companions which are all level 45 and lower... I can't refight the boss due to the 3 hour wait time I now have on them and if I wake them up they get destroyed again. I can't buy more tomes and I am running out of options. Should I just wait the 3 hours or is there a better way to level up my low level companions?
There are many ways to earn Training Tomes, and there are even free "hidden" tomes scattered through the game. There is also the Brawlin' companion task that you can send your companions on to earn them experience while you aren't using them.
If you don't have enough gold to pay Miracle Mitch for healing, sell unwanted pet gear to the Pet Vendors in Circus Maximus. Some of the rare items sell for 1020 gold.
Finally, you COULD try using the lower leveled companions, maybe change your strategy from what isn't working to something that will? I don't know who your A-Team group is, but if your ranged companions are getting flattened, try using some buccaneers. Personally, I think every companion has a place on the team, if you know what their capabilities are.