I'll be going to Tokyo in end Feb with my baby, and I've joined 東瀛遊 package (accomodation: Sunshine City Prince, airlines: CX/KA/JL/ANA, but not UA mentioned in the leaflet) which is the cheapest.
Remember the booking deadline is extended to Jan 26, and the departure date is until end March.
This promotion is listed in the second leaflet: CLICK
I also going to Tokyo early Feb and I booked Keio Plaza Shinjuku thru Farrington Travel. The hotel divided into many rates, it depends whether you check-in during Sun - Mon, Tue - Fri, Sat and whether you take breakfast or not. Also, you can see from the web www.jalselect.com.hk, they also got the rate for many hotels in Shinjuku and Ikebukuro area,e.g. Sunshine City Price at $1050 and Metropolitan at $1180. I will prefer Metropolitan.
I booked the package (5D4N in Sunshine City Prince, Twin Rm w/ bf) at HK$3,799 (HK$4,299 - HK$500 early bird discount) + HK$5xx tax.
I found many people stayed at Toyoko Inn 東橫inn or Super Hotel in Shinjuku or Ikebukuro, while Hotel Grand City in Ikebukuro is commented good as well. They are all under 9000 yen (Semi double) per nite. You can find how to reserve the rooms in cheaper rates in the following forums.
One of the great advantage of Toyoko Inn is that you can make / cancel your booking online at toyoko-inn If you go to Japan very often, they have 100+ hotels in Japan and by becoming the 4&5 club member, you will enjoy a lot of benefits including free stays and discounted stays.
Btw, don't expect big rooms from Toyoko Inn though the rooms are tidy. I stayed in their Ikebukuro, Shinjuku, Sapporo and Nagoya hotels and all are fine for me. Usually it's much easier to get a single room, and you need to book earlier for twin or double.