Unlike at overseas stations where check-in begins only 3 hours prior to departure, at Haneda the check-in counters open at 6:00, so yeah, you should be able to. See Scot's post above.

Alternatively, it may be easier for you to just store your luggage in a luggage locker at one of the stations downtown or near your hotel. It'll save you the time of having to trek out to Haneda and back in the morning. Tokyo for example, in the basement level (B4) close to the Narita Express / Yokosuka Line platforms, has a couple thousand lockers that aren't as trafficked as the main ones on the main level. It'll cost just a couple hundred yen to stash your luggage in one of those for the day, and you'll probably end up transiting through either Tokyo or one of the other main stations on your way back to Haneda in the evening, which shouldn't put it out of your way.