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It was indeed radio-frequency. SAGE used the AN/GKA-5 transmitter and AN/FRT-49 amplifier/transmitter to send target information to the F-106 interceptors, which were equipped with AN/ARR-60 or AN/ARR-61 receivers. These passed data on to the aircraft's MA-1 fire-control computer.
According this webpage the AN/ARR-61 "would check it for validity and proper aircraft address before sending the information on to the F-106 Delta Dart's MA-1 computer". So the system had at least simple checks to prevent the malicious transmission of messages. An attacker would at least need to know the correct address of the aircraft they wished to reroute. However, the system was likely vulnerable to replay attacks. An attacker could record the first update sent and replay it continuously. This would keep the interceptor on the same course resulting in a failed intercept mission. The ground station however used the AN/FRT-49 which is a 20 kilowatt linear amplifier when transmitting the signal. This means an attacker would need a very powerful signal for this to work.
There is more information at f-106deltadart.com, and searching on the equipment designations also finds details.
Some information on the BOMARC integration can be found here, including designations. The search radar is AN/FPS-20, which drives the AN/FST-2 coordinate data transmitter, which sends polar coordinate data from the radar site to the AN/FSQ-7 computer at the SAGE site. That requests height data from the AN/FPS-6 height-finder radar, which sends its data back via the AN/FST-2. However, there's nothing on the designations for the missile command system.