Depending on your hotel almost all of them will hold your luggage until check in time. Given you're arriving at 5:30am you probably will be out into Japan by 6:30. You might be able to get onto the transit before the rush hour really begins from Haneda to Central Tokyo. Depending on where you're staying you will likely be going against the rush hour traffic if you aren't staying inside or near the Yamanote line loop. You'll be going against the crowds heading into then center after getting in to town so it shouldn't be quite as crowded on the way out to your hotel.