I haven't used stunnel so I'll leave that part of the answer to another responder. With regard to WMQ, keep in mind that this will provide you with data privacy and data integrity over the stunnel link but will not give you channel-level services such as WMQ authentication. True, you will have some level of authentication on the stunnel connection itself, but anyone with a TCP route to the QMgr that does not arrive via stunnel will also be able to start that channel.
Your requirement for security obviously includes data privacy. If it also includes authentication and authorization, you might need to use something like BlockIP2 (from http://mrmq.dk )to filter incoming connections on that channel by IP address to insure they arrive over the stunnel link. Of course, there is nothing to prevent someone at the remote end from specifying any channel name to connect to so if you secure one channel, you need to secure them all - i.e. make sure that SYSTEM.DEF.* and SYSTEM.AUTO.* channels are disabled or that they use SSL and/or an exit to authenticate the inbound connection.
Finally, be aware that if WMQ is configured to accept the ID presented by the client then the connection has full administrative access and that includes remote code execution. To prevent this you must configure all inbound channels (RCVR, RQSTR, CLUSRCVR and SVRCONN) that are not administrative with a low-privileged ID in the channel's MCAUSER. For any channels that are intended for administrators, authenticate these with SSL. (Hopefully your 3rd party SW is an application and not an administrative tool! Any WMQ admin tool must support SSL or else don't use it!)
So by all means use stunnel to secure this link, just be sure to secure the rest of the QMgr or else anyone who can legitimately connect (or even anonymous remote users if you leave MCAUSER blank and aren't using SSL and/or exits) will just bypass the security or disable it.
There's a copy of the IMPACT presentation Hardening WMQ Security at https://t-rob.net/links/ which explains all this in more detail.