You can manually take transaction log backup on any replicas of AG. For primary and secondary replica you can take normal T-log backup, only copy_only full backups are possible on secondary replica. I would suggest to take T-log backup from secondary replica this will put less load on primary replica and would also not affect peak time I/O.
In any case log backup chain would NOT be disturbed just make sure that when you take T-Log backup you do not delete it but store it like you do for your normal backups so that you can use it in case of disaster.
In AlwaysON AGs do we take T-Log backups for Synchronization manually or do they happen over the wire (End points 5022 ) . Can some one please simplify this process for my understanding ?
T-Log backup has no relation with synchronization, yes communication happens via endpoints and commit handshake happens via endpoints. For more details read Always On Series