I joined 東XX for 8 day package in late Sep. It is actually a 3D2N package for $4K per adult plus additional stay in Keio Plaza w/breakfast. I end up paying almost $18K for 2 adults + 1 child including $200 extra each for early flight to Tokyo and latest flight to HK. The child requires only air ticket but I think other places could be cheaper for the child's ticket.
I originally planned to book through priceline but they only have limited choices on flights and hotels when my hubby strongly refuse to fly on UA or NW. By the way, price for Keio Plaza through this agent is reasonal.
In conclusion, separate booking for flights and hotels should be cheaper but unless you have lots of time in shopping around. Sometimes, they gives the true price for the hotel only when you call for quotation or go in person and it is quite a different from the listed price on flyer.