Genbukan is a branch of Ninjutsu. It was started by Hatsumi-Sensei's senior student after they parted ways in what has been described as less than cordial. Bujinkan practioners are not allowed to practice with Jinenkan and Genbukan schools per Hatsumi's wishes.
I trained at a Genbukan school for about a year. The instructor was a very good martial artist and we did a lot of full-contact fighting, but that was because it was in his background. The Genbukan system seems to be a lot more formalized than Bujinkan and I think this produces a more consistent quality in the students. I also think they tend to train harder from the other Bujinkan schools I've seen.
As far as fighting goes, both styles use a lot of standing jointlocks and strikes. I studied the Bujinkan system after I moved and no Genbukan schools were around. Both systems seem to be pretty similar with how they move. Overall I don't think standing joint locks work very well against someone really resisting and trying to hurt you. If you're going there to learn JJJ you'll probably be OK, but again I don't think the core joint locking techniques work that well which leaves you with the striking techniques. Whether the stirking works is up for you to decide. For me, I wasn't impressed because in the Bujinkan you are basically discouraged from sparring.
I'd take BJJ before I took any form of Ninjutsu knowing what I know today.
P.S. Go over to www.e-budo.com and drop a message to John Lindsey. He has been doing Genbukan for years and I think runs that site. Also ask about the instructor to make sure they are legit.