There has been several news articles published about a year ago indicating that all agencies at NY Penn will soon be able to talk to each other on the same frequency/radios. So there must be either one frequency (or talkgroup under the Metro 25 system) in which Amtrak PD, MTA PD, and NYPD ALL have access to in order to communicate effectively at NY Penn....I would assume it is the main frequency used there now for all the agencies to communicate. If no one has that frequency, I may take a trip over there in the upcoming months with my scanner and see what I can close-call.
Those articles you read were most likely about the recent amendments to the FCC rules denying "Railroad Police" (Private Police that are owned and/or controlled by non-governmental entities like Amtrak, CSX, or Norfolk Southern) access to the federal interop frequencies.
This was only the first step as every agency would need multiband radios to have one dedicated channel at Penn Station. APD has VHF radios, MTAPD has VHF/700800 radios, NYPD TD has VHF/UHF, and NYPD MTS has UHF radios. Just to name a few. For now they will have to rely on their dispatchers to relay information to adjacent agencies unless they have a MOU (Memorandum of understanding) and are on the same band like MTAPD and APD. Since the recent changes APD can now have VCALL10 and the VTAC channels in their radios (not sure about VLAW31 although they do have it) but that doesn't help them talk with NYPD.
The lead agencies inside Penn Station are MTAPD (LIRR concourse and tracks) and Amtrak PD (Amtrak and NJT concourses and tracks). MTA PD District 4 uses 160.3200 114.8PL inside and TG:6025 on the Metro 25 TRS outside. APD uses 161.2950 131.8PL inside and outside Penn Station. They both have each others channels in their radios and will talk to each quite frequently. APD is limited to VHF and currently doesn't have access to Metro 25. There is no Metro 25 coverage inside Penn Station. Other agencies like the NY State Police don't have a radio system inside Penn Station so they operate on the MTA PD channel. Same goes for NJT PD and DHS FAMS/VIPR except they will use the APD channel.
When it comes to the NYPD, the MTAPD have UHF portables in their RMPs with their frequencies and APD has one or two radios floating around.
During a high security special event (e.g. The Pope Visit) outside agencies (e.g. NYPD) have set up temporary radio systems inside Penn Station.
As far as the National Guard goes like you said I see them with different radios/antennas everyday. I believe the argument is that they are military and not law enforcement and therefore don't have a need for interop, although I'm sure their commanding officers have constant contact to APD and MTAPD via telephone.
What they are doing to build out Metro 25 underground or inside buildings is installing BDAs (Bi-Directional Amplifiers) with antennas outside.
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Penn station is mostly VHF stuff. Put in FDNY VHF citywide with no PL and the old fireground 153.830 no PL. They are both used inside for incidents.
Does FDNY have VHF portables sitting at a location at Penn? This is the case at GCT, there is a box located off Vandebuilt Ave with a dozen or so XTS-3000 vhf radios. Output is 153.83 C.S.
FDNY at Penn Station has dedicated VHF radios at the Command Post in the old taxi lane (31st between 7th and 8th). The latest frequency is 154.5475 167.9PL They also use the UHF HT channel assigned by the dispatcher for box "8171". FDNY battalion chiefs will also communicate from other locations like emergency exits from tunnels using the FDNY 6B Ops channel on the NYC DoITT TRS.