Aaron,
Both sites run JavaScript. That is all I could see in common between them.
When one site goes down, does the other site go down too?
Are the outages happening around the same time every day or hourly etc.? Can you find any pattern in the outages?
Since more than one browser has a problem, I am wondering if it is a DNS Resolution issue. Depending on your replies, we might have you try to ping IP Addresses when you are in the middle of an outage.
Take Care,
Richard