My kids attended the VBS at Bay Area Baptist Church last summer even though we are not members there. They were very organized, happy, energetic staff and volunteers, and a fantastic reception following the program for the parents.
I have found that most churches use the same or one of a couple new VBS curriculum. So, no matter if it is a Presbyterian, Lutheran, Baptist, or other denomination, they are usually teaching the same curriculum.
Now, on the other hand, the staff and volunteers will be different at each church of course. I believe it IS IMPERATIVE that you have a peace from God about the church where you sign up for VBS. Occasionally there are 'volunteers' in churches who are pedophiles. Make sure you meet the leaders and staff prior to signing them up. When you do sign them up, try to make sure your children each have a friend signed up with them so they can be in the same class with together. Remind them to stay with their 'buddies' at all times.
I don't mean to scare anyone away from VBS - I have encouraged my own children to attend at least one VBS each summer. We prayerfully consider which one to attend. Not always the one with the most 'cool activities planned' - one year was a teeny - tiny church with a limited budget. But that year they had really anointed staff members and my kids got more out of that VBS spiritually than any other! The BEST Vacation Bible School is the one in your own home! You can get the same curriculum most churches are doing, or any one you choose (at any Chistian Bookstore)and go through it together as a family throughout the entire summer!!! What a great family bonding experience with eternal rewards! Anyway, have a great VBS experience this year! :D