With the current exchange rate against the US dollar you would find restaurants and other parts of "living" in Tokyo to be a lot lower than they were historically, at the same time Seoul was typically cheaper and probably still is on a day-to-day basis.

From personal perspective I would probably use the points for Seoul, mainly as I feel that the hotel experience (despite being cheaper) would probably be superior, however either way wouldn't be a bad plan. I say this as:

• The hotels in Tokyo are nice and have good breakfasts, but have very small rooms by international standards. The rooms may be of a high quality, but they won't have much space
• In Tokyo there is often a temptation to eat out at the markets for breakfast (e.g. fish market sushi), so you may miss one or two hotel breakfasts anyway.
• I would expect superior service at a Japanese hotel, along with lots of nice touches such as robes/PJs, but you don't really spend that much time in the hotel to benefit from this in many cases
• But the happy hours / lounges have been, generally, more fun and with larger spaces in Seoul (which is used to lots of US service personnel turning up in the lounge and drinking for hours). At the same time, I'd be happy to have drinks at some of the drinking/bar streets in Tokyo that are easy to get to and right next to large stations.

Note, both cities are large and will take a while to get around, so your ability to choose an airbnb at a suitable location for your own trip may be beneficial, and may offer more choice than hotels. I think Tokyo probably has more Marriott branded hotels and choice at different price points.