kimi ryokan in ikebukuro is popular, affordable and clean. halfway between a traditional ryokan and a youth hostel, the rooms are traditional japanese tatami and clean. they have a japanese bath for private use, but it was always in use whenever i've stayed there. no meals, but a hostel style kitchen. it's a great deal, and fills up fast, so book early.
for a more traditional but still affordable ryokan, sakura ryokan is great. family run, they serve japanese breakfast and dinner available with reservation. tatami rooms, japanese bath, convenient to the subway.
for a more contemporary take on the ryokan, andon ryokan is lovely. brand new, the design is gorgeous. the rooms are small, tatami but very modern. small clean showers, and a jacuzzi availalbe for private use. western-style breakfast and self serve coffee are both excellent. andon has a great staff, and is committed to sharing japanese culture with foreign visitors. they even have a tea ceremoney demonstration. since their prices are by the room, rather than per person, andon is affordable for 2 people sharing a room, but not for single travelers.
curious about a capsule hotel? the capsule inn in akihabara is new and seems promising. previously, there was only one capsule hotel for both men and women (in separate areas, often capsule hotels are men only) in tokyo, the asakusa riverside capsule hotel, which is a little tatty, but cheap and decent.