The best indicator of the performance of a web application is the average response time. This metric directly measures how quickly the web application responds to user requests, which is a critical aspect of user experience. The other options, while important, do not directly reflect the performance experienced by the user. Server thread count and server uptime are more related to the capacity and availability of the server respectively. HTTP server error rate indicates the frequency of errors, which is important but not as direct a measure of performance as response time.