Sorry about the late reply but I was just going through all the old requests looking for more interesting stories to read. Anyway I got three recommendations and a C2 you might like. The C2 has a lot of HP crosses but they are clearly marked so they are easy to avoid.
The three stories are:
Two worlds, Two Ninja by
Synica
Naruto is transported to the world of Sylvarant in Tales of Symphonia game.
Bound to Eternity by
Valakun
Naruto receives a 'gift' from Kyuubi on his 18th birthday and ends up later on traveling the world. Crossed with SM and Ranma.
Humane Studies by
Itallia
It's not really a crossover but it does involve a group of ninja jumping dimensions like you are looking for. Basically it's what will happen if a group of ninja appeared in San Francisco, USA.
and finally the C2
Naruto crossover
Hope this helps.