I think this is pretty common.
Going JFK<->LGA is not that bad. You have a couple options. Taxi and shuttle buses. They are only about 8 miles apart, but with rush hour traffic (pretty much all day

), it can take over an hour by cab or shuttle bus. Shuttle buses are cheap, they cost about $5-10. Cabs will cost you $15-20.
Going Newark<->JFK/LGA is a major pain. You can take a cab which will run you over $60 (it's $45 from Manhattan to JFK alone). Depending on time of day, can take over 2 hours.
Or you can take the NJ AirTrain to the PATH, then take the PATH into Penn Station, take the subway to Jamaica Station, and then take the JFK AirTrain to the airport. Probably impossible to do with anything more than a carry-on.
I think the airlines usually give you a good amount of time to transfer, I know somebody who flew out recently and had 5 hours between JFK-LGA and another person has 8 hours. The airlines know this so you would NEVER have to get there in 45 minutes or anything. Welcome to NY!
