The Cyber Commander and Cyber Syncs is a great system but it is almost impossible to see the Commander display out in bright sunlight. If you plan to just use them in a studio this will not be an issue or you could use an old Hoodman loupe to view the display when needed. The older Hoodman loupes were designed for the smaller screen DSLR's back in the day such as the 5Dc and they cover the Cyber Commander screen almost perfectly. I am not sure which Pocket Wizard's you are referring to but if you plan to use the Cyber Commander with Einsteins then you already have full control of them plus a lot of features that you are not going to find in others systems but I would suggest buying a Cyber Sync transmitter to trigger your Einsteins so that you can keep the Commander close at hand to make flash adjustments and use as a light meter.
There are a variety of ways that you could go for integrating and controlling small shoe flashes depending on how much you want to spend and what features you think you will need. If you want the full meal deal of TTL and HSS then you will need a TTL system like the Yongnuo YN-622n or Phottix Odins for Nikon and Nikon compatible ITTL Speedlights. You would use one of their respective receivers to trigger your Cyber Sync transmitter unless you will be using only 1 or 2 Einsteins and then you could trigger each of them with a separate receiver if you so choose. If you are just needing manual flash control then once again their are several systems that would work with your Nikon such as the Cactus V6 which can control the Manual flash output of a variety of shoe flashes or the Godox CellsII-n which you could then use a variety of shoe flashes such as the V850 (TT850), V860N, Wistro 180 or 360 (rebranded by other distributers) and control their Manual flash output with an FT-16 transmitter.
One thing to note is that a flash system like Godox, that can use a separate remote transmitter to adjust flash power, could then be triggered using Cyber Sync Receivers and a CS transmitter thus bypassing the need of another radio trigger system. Also if you have a transmitter with a pass through hotshoe then you might even be able to mount and trigger the Cyber Sync transmitter directly from the camera without the need for a separate receiver. Just something to keep in mind as I do not know all the capabilities and features of the different options that are out there.
I am sure there are more systems that will do what you want to do but I am not a Nikon user so I cannot think of any more Nikon compatible ones off the top of my head. One system that should work and deserves mentioning because it offers some unique features as well as being one of my favorite systems, is the Yongnuo YN-E3-RT/YNE3-RX combo. Although it is designed to work with the Canon Wireless RT system the YN-E3-RT transmitter has a Legacy Trigger feature (turned on/off in the CF) which allows it to work with non Canon Cameras while still controlling and triggering Canon compatible Wireless RT Speedlites in Manual flash mode. With the addition of the YNE3-RX receiver you can expand to those Canon ETTL compatible Speedlites that are non RT such as most of the older EX Speedlites or third party ones such as the Phottix Mitros+ as well as others but too many to mention them all here. The YNE3-RX will also trigger strobes with a sync cord or you could mount the CS transmitter in the hot shoe which would then trigger your Einsteins. Unfortunately I do not have anything but Canon Cameras to test the remote triggering of Einsteins to make sure they would sync properly in the Legacy mode, when triggered with a CS transmitter, when using a non Canon camera.
The only reason that I mention this system is that most of the systems only allow for control of 3 groups and most do not have the capability to turn those groups on/off or at the least not very quickly and easily. Using the <Gr> mode on the ST-E3-RT you have control of 5 groups plus you have the capability to turn each individual group on or off quickly and easily. One other feature about the <Gr> mode in Legacy is that possibly you can expand control beyond Manual flash to Auto Flash by setting a group to Ext A mode (I say this with the disclaimer that I have no way of testing it with a non Canon camera and that this capability would only be available for use with an RT Speedlite with External Metering capability). Holding the transmitter in my hand and testing this feature the flash does change flash output as the FEC is changed but I am going to leave it at that. Of course setting one of the groups to ETTL would not work because there is no ETTL communication between a non Canon camera and the YN-E3-RT transmitter.