determining packet loss over the WAN

I host an application for a customer on the west coast,  the application server lye's on the East Coast, so we do have quite a distance.  The average ping time between the two locations is about 99ms.  I would like it to be less, but I can't control all the hops on the internet.  They have been complaining that their application locks up at certain times throughout the day, I don't see any abnormalities at the datacenter where this application server lye's.  Bandwidth is well under its max, processor and memory on the routers, firewalls, switches, servers, etc are low, and any report I pull shows no alarms or errors.  I also have no other customer complaining, so I don't believe it the datacenter.  I think they are experiencing problems on their side with bandwidth, but they are playing the point finger game.  They sent me output from a network app they use that show response time, packet loss, data loss, etc.  The data loss said 1%.  So now they think there is an issue.  I have always been told that 1% and below is normal.  Does anyone have any recommendations for putting an end to this.  Is there a way I can test for data loss besides just using ping, traceroute, pathping, etc?  Any good explanations?  Thanks.