Best bedside system, unit?

Cambridge Soundworks gear may fit your bill nicely. Check their website for various models.
Bose and Yamaha has table top systems worth a look see.
McIntosh has a two new small systems should Santa have reason to believe you have been awfully nice this year.
Pending your budget there are some nice units to fill your need. Good hunting.

I just got a sonos play 3 for my bedroom, definitely worth considering. I think the 5 has a headphone out.

I just bought a Squeezebox Radio for exactly the same thing as you are wanting it for. It's a fantastic unit!

Another thumbs up for Squeezebox Boom radio. Great unit and alarm clock is programmed to fade in favorite music.

TIVOLI AUDIO

http://www.tivoliaudio.ca/