there are two sewer crystals that aren't in the sewer. both are on auqatos, i don't know how you missed them but when u go through the level like you would the first time, you should run into both. try redoing the level.
If you mean the Crystals you get when you go trough the level the first time and encounter those huge Amoeboids that give a Crystal when you beat 'em, then I got them both already.
I mean in the big Sewers, with the Plumber at the beginning. Using my Map-O-Matic I came to a grand total of 100 Crystals(including the ones from the level), but for the Skill point, I need the last one, and it's not located on my map!!
If it was, then I wouldn't have asked help.
Nevertheless, thank you for your effort to try and help me. As to redoing the level, I have walked trough the level numerous times(up to Slim Cognito's shack, the sub is closed down there)