Hi Dave.
Just got back from a mid April trip (April 6-15, 2008) on Nautilus Explorer. (Great boat also, btw).
Weather: first four days were very windy, and quite rough, which affected viz, divable sites and animal life. We only got to do one dive at the "Boiler", which is (I think) one of the best dive sites, and it was so rough it was really scary boarding the big boat again (see Ken Kurtis's trip report on here for some explanatory pictures). The last 2 days were calmer, bluer (sky and water) and we saw alot more life (out at Roca Partida), more like what one expects based on trip reports on the web.
We were the NE's last trip of the season this year. For every one of those first four days, I vowed never to do a shoulder season trip again. Our trip had waaay fewer Manta "encounters" than I expected. I got to go belly to belly with one once at Roca, and one turned and swam up to me at Canyons before splitting, but that was pretty much it for me - the rest were flybys.
You can get an idea of which trips have good sightings by reading all the Captains's Logs on the NE website - you can get an idea which trips had consistent mantas and sharks and which didn't.
FWIW, we saw jillions (technical term) of humpbacks on the surface, heard them underwater on every dive, and one diver (not me, grrrr) got to hang with one underwater. I gather seeing one underwater is pretty rare though.
It was my first trip though, so I don't have much to compare it to. I've looked into the timing though, and like Alex says, January and February seem like the most consistent, with the December and March trips seeing lots of good wildlife too.
HTH
Taxgeek