I didn't play 64 when it first came out, so I have a less biased opinion based solely on how fun the game is now and with no nostaglia at all clouding my opinion 
IMO, Galaxy blows 64 out of the water. MUCH better music (even if it wasn't orchestrated), MUCH better level design, way more creative, feels FAR more like 2D Mario...
I'm gonna be honest, I hated the dumb exploration in 64 and Sunshine. Hated it. It did not feel like Mario to me.
When playing 64 I was forcing myself to find stars and looking for the easiest ones to get just so I could beat the game. I went straight to Bowser as soon as I got the stars required. I also did not like how 'clunky' Mario controlled.
When playing Galaxy I was so excited to find and play all the stars. I had gotten around 100 by the time I beat Bowser and the game (40 more stars then required) and now have 117 stars. (Still cannot beat 3 stars...) Mario controls fluently and awesomely, perfect.
I'm glad Galaxy took a new design choice, for it is the best game I have ever played. 
P.S. This thread is biased, no option for Sunshine...although no one would pick it
Top 3 favorite games: Super Mario Galaxy, The Sims 2 (PC), The Legend of Zelda: The Wind Waker
