We have always used Freeport Flight Center tel: +1 242 352 7315. They have always been good, and customs have their own little set up in the 'FBO' building. If you can lay your hands on some Bahamas immigration landing slips before you go it will speed things up a little.
Get yourself a rental car organised (usual agents in main terminal building) as its a bit out of town and also if you want to explore (they filmed for pirates of carribean here and the sad looking shell of the Black Pearl from the film is washed up on a beach out of town). They drive on the left, but have US cars with left hand drive so watch out overtaking.....
Hotel wise I would recommend the Pelican Bay Hotel - right in the centre of Freeport so easy walking to bars and restaurants. Has nice rooms. Not on a beach (in the marina area) but you can easily walk to sand if you need it. Don't go for the Windham resort - yes its all inclusive and on a good beach but its truly hideous...