I would be very surprised if the time of day made a difference. I've personally never heard mention of such a phenomenon in discussions with intensive care practitioners (where of course HR and BP are measured constantly). However this is only the case during rest, this paper (on horses) suggests that there is some difference in HR and BP after exercise depending on time of day.
You are right to attempt to control it however, I suppose. It doesn't matter when you take your measurements, as long as you take them at the same time each day.
I would say that one of your first suggestions of taking the measurements almost immediately after waking. Of course you would have to be relaxed as you assembled your equipment then rest for a few minutes in the posture you have chosen (this will matter) before taking the measurements but otherwise I can't see you having too great a problem.
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