Unless the situation has changed recently (and I can't check cos I don't have a 3GS), then the OP can go to 4.1 iCrank. As Jmills87 correctly pointed out, Apple are still signing 4.1 for 3GS (not for any other phone). Because of this you can still install it whenever you like. I haven't seen any reports that they did close the window... It is a strange anomaly and an exception to the normal rule, but if Apple provide the signature it will work.
Then stick your iPhone in DFU mode, start iTunes, and shift-click (option-click on Mac) on the restore button. This will allow you to select the 4.1 firmware file you just downloaded and it should install OK. If you previously messed with your hosts file (which it does not sound like you did) then you should put it back to normal first.
I can confirm Apple is still signing 4.1, I just saved a 4.1 SHSH on a friends 3Gs yesterday, it only seems to be for iPhone3G/3Gs and iPod Touch 2g/3g though.