If you want a cheap, good massage - that's hard to find. Those usual spots that people talk about, don't really offer a 'decent' massage. You can expect to pay about 8,000 yen for a very simple massage with a very 'rapid' ending.
Some of those shops have also recently changed their policy on accepting foreigners. Some still are accepting foreigners, others are not.
I'm at work and don't have the links handy for the ones that I do know of... I'll try to remember to post them later. Plus, I'm moving this post over to the massage section.