whining in crate UGH!

How old is your puppy, and how long are you expecting her to hold it for? Maybe she can't last that long yet, and in that case, you could either take her out for her last pee of the night later, set your alarm for before she usually starts whining so that you can get her up to go out, or get up in the middle of the night and take her out.
My other question is, what do you do with her after you take her out to pee? I found that my dog was whining, not because he had to pee, but because I had been taking him out to pee, and then going to sleep on the couch with him. I guess he figured out I would wait for a pause in the whining, then come get him out, and we'd come in and sleep on the couch. My method for solving that was to have him sleep in my bed the whole night. Now he sleeps until whatever time I feel like getting up in the morning.

yeah, I'd think the whining maybe is indicating that the little guy's gotta go!!
Setting your alarm for like 5:45 and taking him out to pee and putting him back might help stop the whining for your attention to his matters of pee....
dogs have internal clocks, much like we do...
I'm not a great one to advise on crate-training... though I have done it for a short period of some of my dogs' lives... like a week or 2 til they are trained not to go in the house, but actually my dogs also sleep in my bed... sometimes I think i'd be MUCH more comfy sleeping on the floor! 
and my back, from being crooked all up in the bed to allow for the pup bodies at my feet etc, would probably thank me if I did sleep on the floor!  lol

My little guy was only sleeping for 3 hours at a time when I first got him.  Now at 3 months he'll sleep around 8 hours at night.  My solution was to move his crate into my room and position it so that he could see me sleeping.  That stopped the every 3 hour whining.  During the first week off sleeping in his crate in my room he'd wake up around 5 (midnight was when he'd usually go to bed) and I'd very calmly take him outside without speaking and let him pee.  I'd then take him back inside give him a treat ALL WITH NO VERBALIZATION and then carry him back upstairs so i could sleep for another 3-4 hours.  I'd place him in front of his crate and he'd walk in and lay down because he was still groggy and not riled up from me speaking to him.  That only went on for a week and like I said now he's sleeping like a log for 8-9 hours a night, thankfully.  So if you can put up with a week of interupted sleep I think you and your pooch will be happy and well-rested.
 
Good Luck!
Lee

Maisy is about 8 months old. i thought maybe she had to go, but i've tried taking her out to go potty, but a lot of the time she doesn't need to go. I usually give her breakfast and play with her a bit after she goes outside....that could be it. I do have her crate (wire) in my bedroom set up where she can see me sleep, because she came from a rescue that got her from a pet store, so the whole cage thing was a bit scary for her at first. I'll try some of these suggestions! Thanks, Erica