Supposedly NOAH makes a bigger profit than New Japan these days, and they seem to draw better too. If NJ grosses more per year, than it's because they're running bigger venues, so there are more tickets available. But as far as the percentage of tickets they're selling, NOAH is probably better. If they ran bigger venues more often, they'd beat NJ in gross I believe.
Dragon Gate is probably #3. I don't know any specific numbers, but based on what I've seen, they draw a lot better than AJPW. But AJ runs bigger venues than DG, so it might be another NOAH-NJPW comparison.
As for spin-off promotions, Zero-One started as Hashimoto's promotion when he was "retired" in New Japan. They eventually brought in Omori/Tanaka/Otani, and then Hashimoto cut his ties to the promotion, leaving those 3 and others. They don't draw well at all, and their product is AWFUL, but somehow they stick around.
Big Mouth Loud is a shoot-style spin-off from NJPW, with Shibata and others. King's Road is a faction from AJPW. Dragon Door is Ultimo Dragon's new promotion, after he was forced to leave Toryumon/Dragon Gate. Then there's Osaka Pro, led by Super Delfin, which was a spin-off of Michinoku Pro. Kind of funny considering how small-scale Michinoku Pro was at the time of the split. These promotions aren't really affiliated with any others though. Zero-One I believe was backed by New Japan early on, but not anymore. The rumour was that DSE was backing Zero-One MAX lately, but I haven't heard much more about it.