Checking that this is what you mean :
You have stunnel bound to port 6666 (localhost:6666) and you have tor bound to 9040 (localhost:9040). You want it so your web traffic will go THROUGH stunnel (so destination is localhost:6666) but the OUTBOUND traffic FROM stunnel (with inbound traffic originally from your client redirected to stunnel) should be DESTINED to tor (localhost:9040) ? Is this correct ?
If so, and I am thinking clearly enough (it is just 7:00 and I've been awake far too many hours for a difficult night), this is indeed possible (the reverse is, too). You need to masquerade the destination address (and indeed port) based on the source (address and port (you don't have to specify both, I might add)). Something like this:
iptables -t nat -I PREROUTING -p tcp --sport 6666 -j DNAT --to-destination 9040
If this is not what you mean (or alternatively I made a typo, am not clear headed or being an idiot in some way (in all cases showing myself to be a user as everyone is!), if any it is probably the latter) then please respond. I'll see about enabling email notification so that I see the response. If I don't, however, I apologise in advance.
As an aside: unless you have a final rule in each CHAIN (not table, just as an fyi: a table is filter, nat (which I specify in the above and indeed it is necessary), etc. and CHAIN is INPUT, OUTPUT, FORWARD and others created by the option -N) you shouldn't have -P ACCEPT ('that which is not explicitly permitted is forbidden' and similar wording - i.e. have DROP). The exception is perhaps OUTPUT (but depends on what you need, in the end). However, when dealing with interface 'lo' you'll want to ACCEPT all traffic always, in any case (i.e. specify -i lo and -o lo, depending on chain, and jump to ACCEPT). Of course, maybe you're behind another device but still best practise to not accept anything and everything! (I should also state that you have different chains per table so yes you can specify different tables but the policy is for the chain IN that table)
Edit: something else: no, you don't have to deal with SNAT when you want DNAT and the reverse is true. Anything to the contrary is a misunderstanding. The reason is you're masquerading the CONNECTION. As the man page shows:
It specifies that the destination address of the
packet should be modified (and all future packets in this connection will also be mangled), and rules should cease being examined.
Edit:
If I understand you (now) you actually have two interfaces involved. Or more specifically you need the following:
You have a service you want encrypted. This is tor. Now, you're using stunnel to do this. To this end you want stunnel to forward traffic to tor. Is this right? If yes, then know that stunnel has the following directives (I actually use similar for something else). Here's a mock setup of a service.
[tor]
accept = 6666
connect = 9040
In addition, just as a note: connect can also be a remote address (remote address implies an external address (with port) or even a certain interface (by IP and also with port) on the system (I use external in the sense of you specify ip and port rather than just a port). Furthermore, accept can specify address (with same rules: ip before the port (except that it is obviously on the local machine so no external IP)). You could explain it, perhaps, as stunnel is where the service would bind to except that the service is stunnel and the service it is encrypting is elsewhere (shortly: the bind(2) call allows specific IP or all IPs on the system, and you're basically configuring stunnel to do this).
(And yes, you're right: the sport should have been dport.)
IF this is not what you need then I do not understand all variables. In that case, if you can elaborate on which interfaces (this includes ports and which service per interface) are involved as well as clients involved (and where they send). Because it is a lot more helpful if others know EXACTLY what you need than infer certain parts. Makes it much easier to solve a problem if you know what the problem is entirely. Maybe I've been dense and I should put together it all (and I admit sleep problems - which I have for a long, long time - does not help that, but...) I haven't, I think.