All three are correct: however, in everyday English, to indicate that there is some uncertainty about the exact time, we would normally place 'about' before the time. e.g.
He estimated the time to be about 3:00.
He reckoned the time at about 3:00.
He guessed the time was about 3:00.
In informal speech 'about' may be replaced with 'round about' or 'around about'. Adding the extra word before 'about' does not change the meaning in any way, and its use is not advised in formal speech.
Of the three sentences in your question, the least credible is:
He guessed the time was about 3:00.
"To guess" means to provide an answer or opinion about something when you do not have sufficient information on which to base your answer. You may guess right, but you are even more likely to guess wrong.
"To estimate" and "to reckon" both imply that the person has put some work into arriving at an answer, and that they have made use of whatever information was available to assist them. "To reckon" is probably the more credible term of the two as it implies that the available data was included in some form of computation or calculation in order to arrive at an answer.