NCU, despite what the software says in the various palettes that open up in NewtonOS, does not work via IRDA. I think it may have been a planned system update that never happened. The IRDA problem, as I recall, is complicated by the fact that there are different IRDA standards, apparently, in different PowerBooks and Mac desktops/towers (e.g., PowerBook 190, Pismo, LC630, Performa 6400), but the bottom line is that it's not going to work. There is a patch for the Newton's IRDA, but it does not enable IRDA synching. What the point of the patch was I have never been able to make out; the write-up in in Attic Geek. I have actually tried it as a fix for the IRDA problem — thinking that IRDA would be the most elegant solution of all — and it was a waste of time.
The real options for networking between the eMate and the Wallstreet begin with a serial (Mac printer) cable, followed by localtalk/PhoneNet cabling. It would also be possible to use an ethernet PCMCIA for the eMate, or a couple of compatible wireless PCMCIA cards, and do it that way; or, if you wanted to work with a machine in OSX, there are also Bluetooth solutions and open source versions of NCU for OSX. And then there's the modem option; most PCMCIA modems will work in a Newton, and I believe that connection by modem even works under Apple Remote Access, so there is something to be said for this option.
Most of this I have never tried, with the exception of Wireless PCMCIA (which I have use to connect via Appletalk with a Pismo running 9.2), so I can't vouch for the robustness of, say, the Bluetooth option. Personally, I use and would advise you to go with the serial cable or with PhoneNet, which means among other things that you will have a continuing use for the Wallstreet.