32.768 khz crystal for time base?
Seems to me you're most interested in reducing electromagnetic coupling from counter (and its display of frequency) to a RF-sensitive circuit (receiver?). The time-base oscillator is just one source of RF. Counter chains and display drivers are other radiating sources. Use a metal-case crystal (like HC-49) and ground its case.
 Integrate your time base into a microcontroller that also drives the frequency display. A crystal-controlled microcontroller master clock can also serve as the counter's time base. The tiny microcontroller area is easy to isolate, bypass, and shield. Discrete counter chains of chips are to be avoided.
Use a LCD display of frequency, rather than LED or other high current displays. Transient currents to each LED segment radiate RF energy. Sometimes choosing a high-frequency crystal allows you to place its frequency in a remote out-of-the way spot that will cause you less grief. Harmonics of a low-frequency time base can cause grief over a w-i-d-e frequency range.