Yep, those puppy weeks (not really years for dogs) can be difficult to figure out for both pup and owner. I know how that works because we've got our own little guy who had to figure out his schedule as he matured.
First off, young pups are way more likely to sleep happily then older guys. For example, when we first got our ferret kit (they're like little puppies in many ways) she slept on our lap like a sweet little thing. Then, after a few weeks, she never settled down even once while spending time with us. No more cuddles, just running around and exploring.
Also, puppies are really smart. If they see they can wake you up, they may keep trying it. Just like in Lady and the Tramp when young Lady is barking for attention and she gets it, they will learn a schedule that waking up at night is part of their new routine and will need trained out of it.
Another thing that can make dogs behavior a little messed up is with an orphan doggy. I know this because we've had our own share of pups come through our doors (we pet-sit) that were taken form their momma at too young an age and they often had behavior issues because of it, including aggression (which you mentioned) and possibly a dependency on human attention (crying at night because they feel lonely).
Another option could be hunger. Puppies that are growing need three or four meals a day, and some breeds can suffer from low blood sugar if not given food often enough. Try a nice meal before night, which may make him need to go but also will give him a reason to doze while he digests.
Next could be issues with his allergies or medication. If he is itchy it could be keeping him up. Also, some dogs react to medication in ways others don't, so perhaps his meds are making him restless.
Another thing that is a BIG help is walks. We learned real quick with our dogs that if they go without enough walks they will whine, bark, fight, and even get obsessed and fearful about things they wouldn't naturally. Our new puppy is a herding dog mix and has so much energy that it takes multiple walks each day, from morning to night, to get him tired enough for a happy, healthy sleep.
Try a nice long walk or jog, not a stroll but a fast paced walk, just before bed time and see if it helps him sleep through the night.
Another cause could be a crate that is too cold, hot, or small. A growing puppy can soon find his bed half the size it was when he first came and temperature changes can throw things off as well. Also, make sure that he has a comfortable blanket inside to snuggle in. A blanket draped over the crate, making it dark and secure, but also help him calm down, since its more like a mother's den then.
Is he the only dog in the house? Puppies that are raised away from other dogs can become very human dependent and when they are left alone at night get lonely and scared. If you have other dogs, keeping his crate near to where they sleep or even locking him up with them in a room might help. While another puppy may just be over-whelming, getting a calmer pup who can play with him and snuggle with him can help a lot with behavior problems and separation anxiety.
If your pup keeps crying at night, let him out nice and calm, let him use the bathroom and then try to take him on a quiet walk. Offer some food (not treats, this will only praise him, but a meal) and then return him to his crate without a fuss. Try covering it up, moving it to a new location (away from you or closer to you) and then see if he can settle down. Again, it can sometimes take a week or more for a puppy to get into a new schedule or to figure out what his growing body is telling him. Don't give into his crying if it is just to manipulate you into giving him attention, but also watch out for any causes that could be avoided.
Last but not least, some pups may change their sleeping habits because of a change in environment. If your work schedule has changed, if someone just came home from vacation, if you or your kids are waking up earlier for school, if the sun is rising earlier or setting later, if there are storms at night, or even night sounds that weren't there before such as a new resident raccoon may have set him off and made him unsure how to react.
Sorry for the long post, but I hope this gives you some ideas and things you can try to help you get the sleep you need.
Best of luck. : )