Every time I tune my electric guitars by ear, the B and e (sometimes G) strings always end up being way to sharp. When I tune them down and try to match them up with the lower strings it just doesn't sound right. Eventually I just pull out my tuner and my guitar sounds like it should. It gets pretty frustrating. Anyone know what might be going on?

Get yourself a tuner. Those snark tuners are really good. I never tune by ear have always used a piano or tuner.
Tuning by ear takes practice. Use a tuner or a piano for now to begin recognizing the tones at which you need to tune to. Practice using your ear as a tool, being able to distinguish tonalities on your instrument but for now just practice internalizing each string tuned note.