The two parameters are completely different. Maximum segment size (MSS) refers to the maximum number of octets that may appear in each transmission. The window size indicates how much temporary buffer the receiving host has set aside for received data that has not yet processed.
The MSS option announces the maximum received segment size that the sender of that option is expecting. It is made during the initial connection setup only. For most Ethernet implementations the MSS is 1460 bytes, which is the maximum Ethernet frame size of 1518 minus all the OSI Layers 2, 3, 4 header information. One of the first troubleshooting steps to take when having difficulties establishing and maintaining a TCP connection when no errors are present might be to reduce the MSS.*
*Source: Network Maintenance and Troubleshooting Guide, Second Edition, by Neal Allen.