Is the Indian museum where indians well was?

If you're referring to Indian Wells, the place on Hwy 395 with the Indian Wells brewing company, no, the Indian Museum is not near there.

I'm not sure I would call the Indian museum about if thats where the well was or wasn't and where it mit be

I believe there was a natural spring on-site at one point (the buildings were built around it).

This was back in the early 60s