While yes, the flight arrives right before the traffic rush-hour, its not so bad that one should avoid the flight altogether. Tokyo Haneda is extremely well connected and there are plenty of options to get to ones hotel.

The Tokyo Monorail if one takes the express, takes them directly from the terminal to Hamamatsucho Station. As it makes no stops, you are only competing for space with other fellow travellers. Rush hour doesn't preclude you from taking this option and should make minimal effect on its crowdedness.

If you are booked in other parts of the city, one can also consider taking the many Limousine Buses, which are fixed fare and should take the passenger directly or close to their hotel. Once again, since the fare is fixed-fare, rush hour really doesn't factor here aside from maybe having to spend a little more time in traffic but you've got AC, a cushy seat, and a great window of the city while you make your way. No big deal really.