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In this particular case, I assume that you are able to interact with the customer to obtain some additional information for troubleshooting. I've included a small set of questions that would help you isolate the issue from A to Z. It's not 100% exhaustive list but certainly covers the major issues that would occur to cause this problem.
 Step 1: Have the customer connect to the other ISP and access the website to verify that the website is up and functional. This allows you to verify two things in a single step: If the website is accessible via the other ISP on the computer of interest then you can assume that there is not a hardware issue with the customer's PC and the website is actually up; alternatively, you can check the website's availability yourself using a computer that has Internet access. However this doesn't provide assurance that the customer's PC is in working order.
If this test fails, then you have definitive proof that your ISP is not to blame for the issue and the case can be closed.
Step 2: If the test doesn't fail, then your next step is to have the customer connect to your ISP. Once connected, obtain basic connectivity information to verify that the ISP connection was successful. Have the customer open a command prompt and type ipconfig /all. Capture the IP address, subnet mask, default gateway, and DNS addresses for the connection. If the connection wasn't successful then follow procedures to renew the IP and troubleshoot connectivity problems.
Step 3: Once connected, verify that basic internet service is available by going to a universal site like www.google.com. This step verifies that most everything is operational within the customer's connection. If it doesn't work then you're back in the basic connectivity issue.
Step 4: After verifying basic connectivity is working, have the customer access the website that wasn't working. There are two basic reasons why this website wouldn't work when www.google.com works: DNS or routing issues. To continue with the diagnosis, have the customer open a command prompt and type nslookup www.mywebsite.com . (NOTE: be sure to substitute www.mywebsite.com with the website that isn't working).
If DNS is working properly this command should return: (go to step 5)
C: >nslookup www.mywebsite.com
Server: dnscache01.stsn.net
Address: 172.16.2.5
Name: www.mywebsite.com
Address: 72.51.27.51
If DNS is not working properly this command returns: (go to step 6)
*** DNSserver.metalchick.net can't find www.mywebsite.com: Non-existent domain
Step 5: If DNS is working properly then the fun really begins. Assuming ICMP is available on your network, have the customer attempt to trace route the IP address. Trace route provides you per hop information about the route that the customer's PC is taking to arrive at the website. If you see something like below, you should check with the router prior to the last hop to identify why it's not providing the right route/connectivity. The ISP should have documented procedures to check the routes and interfaces for issues around this issue.
C: >tracert 72.61.27.51
Tracing route to 72.61.27.51 over a maximum of 30 hops
1 8 ms 8 ms 6 ms 10.26.116.1
2 22 ms 16 ms 13 ms 147.225.203.69
3 91 ms 28 ms 24 ms 152.161.241.26
4 329 ms 168 ms 202 ms 72-255-0-1.client.stsn.net [72.255.0.1]
5 310 ms 90 ms 29 ms 208.254.24.170
6 25 ms 26 ms 26 ms 206.112.64.4
7 * * * Request timed out.
Step 6: This is a DNS issue. Contact the DNS administrator to see if there is some known issues with DNS. I would also see if there is a secondary DNS server that you can have the customer connect into with accurate name resolutions.
In summary, there are approximately 3 major issues that I can identify with this process. First, you would want to identify whether or not it's an ISP issue at all. By verifying the client PC and the website configuration, you can eliminate external causes for the problem. If the ISP is having issues, then you have two major reasons why certain websites would be accessible and others would not. DNS and routing issues would prevent the customer from reaching the website of interest on your ISP. Good luck with your troubleshooting, and I hope that this provides some better guidance for troubleshooting in the future!
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