Park Hyatt
Grand Hyatt
Peninsula
Ritz-Carlton
Four Season (the main one)

The only IC property I considered on my last Tokyo trip was the HI at the airport on my last night as its the nearest hotel. And, for the (very little) money its a good property.

Seriously ... the best deal in Tokyo in my view is to get 6,000 Hyatt points and use them for a 1-4 night suite upgrade award at the Grand Hyatt (Park Hyatt is even plusher but not in a great spot for tourists). Beautiful wedding chapel at the Grand Hyatt as well!

The Peninsula and Ritz-Carlton are both brand new and should have all the bells and whistles I'd want from my honeymoon.

None of the IC / ANA properties seem especially well regarded on here - I am back in Tokyo in May and, despite my RA status, I haven't even considered them. If I can get availability I'll be doing a suite upgrade award at the Grand Hyatt.