First, try other websites. Ideally, ones that are logically close to the website that you're testing. For example, if the website is hosted on AWS, try other sites hosted on AWS. You can use traceroute and the like to determine where the website is logically located.
Second, look at logs. You can see from apache logs when a request came in, and possibly how long it took to complete, depending on what's being logged. You may be able to follow a request from apache/the web host to the database and back.
Third, and most import, when doing performance testing, you need to isolate the thing being tested as much as possible. Ideally, you shouldn't be crossing the internet to get to the web app, or parts of the web app. You should have a dedicated host, dedicated client machines, and a LAN connection that crosses as few boundaries as possible between the two. If you have to test a remote site, you should make sure that the client machines are at that site as well. If you're using AWS, set up client AWS machines. The more variables you have to deal with when doing performance testing, the harder it is to make a valid conclusion when testing.