Hello drumatix,
There surely are onsen that would accept people with tattoos. However, the subject is rather taboo, and definitively no onsen will advertise the fact that they have such policy!
If someone who has tattoos could have been accepted in an onsen, he probably could share his experience. It is not my case, though.
You best chance to soak in an onsen is probably to reserve a private bath in a ryokan. This site :
www.kashikiri-onsen.com lists many kashikiri onsen - bath you can reserve for a certain period of time. Some are outside baths, so the experience can be pleasant, too.
sanji