Since I started playing, I sided with Mr. House. I finished Volare! and I helped the Omertas (I sided with the bosses). Afterwards I was apparently (about to be shunned) by New Vegas. I went to Mr. House, and told him everything. I failed Don't Tread on The Bear and prior to this I had failed the Legion one and now I am hated by them and marked for death. He wants me to kill the BoS now, which I do not want to do because I personally think they are awesome.
Thing is though, I made a save BEFORE I completed the Omertas quest and talked to Mr. House and failed Don't Tread on The Bear. Is it to late to work with the NCR?

If you failed don't tread on the bear then yes, I think it is..
However Yesman can't die and you don't have to kill the BoS for him unless you want too.