I stayed at Harumi Grand Hotel in Harumi, Tokyo - very close to Ginza and Tsukiji Fish Market. We got the Delux Twin room for 9,000 yen (4500 per adult x 2) and 2 kids free. It comes with free breakfast. It is extremely hard to find a room to accomodate 4 in Tokyo besides TDR area and this is the only decent room I found through searching (in Japanese) with reasonable price. (The other option was Hotel Sardonyx in Hacchobori, but it was more expensive and the beds were slightly smaller (140cm)) Harumi Grand Hotel had a big room (considering in Tokyo), big beds and big enough for 4 of us.
What I was looking for in a hotel room was somewhere close to the Fish Market (since the time of the Tuna auction, there are no bus/subways running and didn't want to pay a fortune on a taxi... , but because of the recent event, the auction was not open to tourists when we when there... Oh well), accomodates 4 and a reasonable price. We only stayed here for one night.
The room was not a non smoking room, but they had an air purifier. At first, I noticed the smell, but after awhile, it didn't bother me at all.
The location is not that great if you are coming from Narita. We took an airport limousine bus to T-CAT (Tokyo City Air Terminal), then Taxi for about 20 minutes. After the initial hasstle, it was great. There is a subway station in about 5 ~ 7 minutes walk and was about 15 minute walk to the Fish Market.
If you are looking for a good price, you should wait until about a month or so before you're planning to stay there. Price will drop pretty good around that time.
Not the greatest hotel in terms of location and condition, but was good enough for our needs and the budget.