Firstly, thanks for the recommendation Tippytoes12.
In Lembeh, if you are not staying on the island, early morning transfers to the airport by car should be no problem. Many guests do RA along with Lembeh and from Black Sand, guests leave ~4:30 am and take 1 hr 15 -30 minutes to get to the airport. Once the Manado-Bitung toll road opens, the driving times should be cut in half (it was supposed to open last month, but this is Indo). Getting to the airport one hour ahead of takeoff is fine in these parts. The roads are clear in the morning and the early flights tend to take off on time. Flights tend to be delayed more as it gets later in the day. If you are intent on staying near the airport we recommend the Novotel, which is ~15 minutes from the airport and you thus avoid the bad Manado traffic.
February is technically in the rainy season, but for the past two years it has been quite dry in February. Even if it rains, there's little runoff into the strait, so visibility is not affected much at all. Between early December and May, storms can come through, stirring up the waves for up to a week at a time in Bangka and Bunaken, but storms don't affect Lembeh. I'd recommend splitting your time between Bangka and Lembeh simply for more variety and as insurance if the weather turns on you.
February is technically the Low Season in North Sulawesi, so it should not be crowded. One thing to take into account, wherever you stay: How many people are on a diving boat? Folks travel a long way to get here and most resorts have 8, 12 or even more divers on one boat.The bigger the group, the higher the chances that you'll be swimming around in a cloud of sand kicked up by others. Guides try to keep diving groups apart, but on popular critters there can be a lineup if you are in a larger group. That's why we limit our boats to four guests per group with one or two guides.
Hope this helps.