For me it's between Super Metroid and the first Metroid Prime. Prime was just a great 3D experience of metroid.
Super Metroid is a great game, I haven't played through it in years now but I do remember it being incredible. Super Metroid at the time was such a leap from the original. The sound, environment, mapping, it was all just incredible.
If you have the means, I would suggest trying the original Metroid. If you prefer a mapping feature, look for a GBA and get Metroid Zero Mission. It is essentially the original metroid game + a bit of stuff that ties the original Prime game in. In Prime you're told that Samus was raised by the Chozo on Zebes. The original metroid doesn't have anything about the Chozo in it, but Zero Mission does. Ties it all together.
Super Metroid is a must play though.