I've stayed at both hotels in the past, I don't think I'd stay at the Holiday Inn again (it was the Courtyard then). The tower rooms were OK, but our last stay was in the wing of the hotel. We had 3 rooms, all smelled musty, the hallway was musty smelling also and you could easily see that there was a water leak inside of the hallway wall since the drywall was falling off! The air conditioning wasn't good at all and very loud, I had asked 3 times during the week to have it looked at. Each time I was told it was fixed, NOT! Luckily I had the $20.03 rate so I wasn't too disappointed. The previous stays there were always nice, but not the last one.
We have also stayed at the Best Western a few times and have been very happy there. It's strange but even when that hotel was full it kinda felt like we were the only ones there. All the rooms have balconies and if you get the side facing Epcot you can see the fireworks from the balcony. My vote is for the Best Western, we weren't dissapointed yet.