I would take Dave's advice and check both. Find the best price via the online companies like Hotwire, Orbitz, Hotels.com, Travelocity, and Priceline etc. Then call the "Central Reservations" 800 number for the hotel chain and get a quote. Then there is one more step..call the hotel itself and get a quote. Sometimes there will be a price difference and Central Reservations will beat the hotel and the online companies.
Another thing to be aware of is that some of the specials and the lowest price rooms are only available by paying up front and they are non-refundable. Whereas a quote and confirmation is higher for an unpaid 6PM room hold.
Most importantly regardless of how you book is to get a confirmation number and confirm your reservation with the hotel directly. I once booked with an online service (not mentioned) and the hotel didn't have my reservation. Thankfully, I called ahead of time to confirm and they got it straightened out.