When we're talking about what hotel you stayed or are staying at, I understand the preposition of choice is "at" rather than "in." 

1. Use "stay in" with large areas such as big cities, towns, countries or continents or streets, areas, zones; means of transport: plane, car, bus, train, ship...

2. Use "stay at" with relatively smaller places: flats, houses, hotels, restaurants, clubs, banks, theaters, cinemas, airports..; some points (điểm): at the corner, at the bus stop, at the door, at the entrance, at the end of the road, at the crossroads, at the front desk...