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As Richard alluded, the best option from NRT to the Asakusa area is probably the Keisei (not JR) airport train. It arrives at the Keisei-Ueno station, right across the street from the big JR Ueno Station and the equally big Ueno Park with all the museums and galleries. There are more than one type of Keisei train. The most comfortable, fastest and easiest is the Keisei Skyliner but it is also the most expensive at 1920 yen (about $18.50.) The Keisei limited express is a bit slower, makes more stops and does not have reserved seating but is only 1000 yen (less than $10.00.) I always use the Skyliner for the reserved seats and the comfort. YMMV.
From Ueno, you could stay in Ueno, taking a cab (1500 yen +/-) or the subway to Asakusa (2 stops.) Nippori is also nice for "older Tokyo" and is only 1 stop on the Yamanote Line from Ueno.
You could also stay in Asakusa, which would involve the same cab or subway ride from Ueno on your arrival and departure but put you right in the middle of the sights. If luggage is minimal, I always use the subway. For carrying much baggage, use a cab.
For inexpensive stays, here is a website I trust:
http://www.japanhotel.net/ .
They list a bunch of lower-cost options -
http://www.japanhotel.net/data/pref/...asp?Area2=UENO .
I see they stopped listing my favorite Asakusa stay:
http://shigetsu.com/e/index.html .
The Shigetsu is a hybrid ryokan - hotel and is a gem. It is also a bit difficult to find without a map. There is a printable map on the website.
JR