Define inexpensive? What's the budget? You can go as low as $60 a night for a closet of a room, or splurge a bit more and get a nicer room in a nicer location. If you consider ground transportation costs, time wasted, etc., it may be worth more to get a nicer room.
Also, Tokyo sightseeing depends on your friends' tastes - the city is very much separated by that, neighborhood by neighborhood. Highly suggesting compiling some ideas.
Lastly, getting to HND is not a big deal, depending on where he ends up staying.
http://www.japan-guide.com/e/e2164.html
http://www.wikitravel.org/en/Tokyo