I have a skype type of application and I want to check the packet loss for that application. Can anyone suggest me the best tool for the same.?
Well it depends, and to get the best answer you will have to decide where and how do you want to look at packets.
The best place to look for packet loss is the application itself since packets can get lost inside the application or on their war from the OS network stack to the application. Skype for example shows some of this information in the "Call Technical Info" windows.
You an look further up the pipeline, but this will require the packets to have a sequence number or time stamps (or both) otherwise you will not be able to identify the loss.
Jailbroken IOS devices can run a sniffer program on the device, or alternatively you can listen on an atached wi-fi, or use "Remote Virtual Interface" to listen on a USB tethered PC.