Taking a break from diving Philippines in late Feb to go winter birding in Hokkaido. Right now I have the option of one more day in Kushiro (five nights total then I think) or spending the extra two nights in Tokyo with one full day in Toyko. The flight back to MNL would be at 9:30 ish from Haneda. Yes, I know it will be cold.
We would be arriving on a Thursday and leaving on Saturday morning. I have been to Toyko a couple of times, mostly on the way somewhere else.

What would be your suggestions for our day in Tokyo? I'm looking for among other things easy access to and from Haneda. Mostly I like wandering around. I was thinking about Shinjuku but discovered it was farther from Haneda than I had thought. NB. I'm 79 female and I do tire easily. OTOH, I have navigated Tokyo trains and train travel through Japan fairly easily.