A widely used TCP protocol is originally developed for wired networks. It has many variants to detect and control congestion in the network. However, Congestion control in all TCP variants does not show similar performance in MANET as in wired network because of the fault detection of congestion. In this paper, we do a performance comparison between TCP variants NEW RENO, SACK and Vegas in AODV and DSR reactive (On-Demand) routing protocols. Network traffic between nodes is provided by using File Transfer Protocol (FTP) application. Multiple scenarios are created and the average values of each performance parameter are used to evaluate the performance. The results show that TCP variants perform better in terms of throughput and Packet drop with DSR routing protocol compared with AODV routing protocol. TCP variants show a lower Jitter in AODV compared with DSR.