I don't know of anything that I would do in Niigata at that time of year that I couldn't do in Nagano. Both have mountains, snow, hot springs, soba and sake. To me, Niigata is just a bit flatter and snowier. For some reason, I dislike many of the famous brews from Niigata, but that's a matter of personal preference. What is it that attracts you to Niigata?

With regard to snow boots - What are you planning to do? If it's just walking around downtown Takayama, you can probably get by with sturdy shoes. But if you're going to the villages in the mountains - Shirakawa go etc. (and I would strongly recommend that you do) - then yeah, you should bring the best boots you have. The snowfall can be very deep. I think people make assumptions based on the latitude - but this region has snowfalls comparable with places far further north. You'll find the exact data online somewhere.