In Rioja region, where you stay largely depends on whether you have your own car or are you going to rely on public transport. Rioja is best visited in a car as most of the region is made of small villages with unreliable public transport.
If you have your own rental car, location per se does not matter. I would suggest a stay in a vineyard or a bodega. You have plenty of options, probably you can start with this site. There are vineyards all around and hence it is not necessary to be very particular. If I am forced to name one hotel, it will probably be Eguren Ugarte
If you are looking to stay at a winery, then Hotel Marqués de Riscal ought to be your first choice. It is a luxury resort - a place to see and be seen.
If you do not have access to a car, make Logroño town as your base station. You can visit the wineries using the vinobus or book yourself into one of the winery tours. I would suggest start your search by checking Airbnb listing of vacation rentals in Logrono. If you want a conventional hotel, you can check Marriot run AC Hotel La Rioja hotel. If not Logroño, the next best option is to stay at a bodega in Haro, a much smaller town than Logrono but full of wineries.