Much early thinking about what became the laws of motion in the Principia, including the third law, can be found in Newton's "Waste Book". It is a notebook started in 1665, and it is discussed by a number of authors, including D Fraser (2005), "The third law in Newton's Waste book" (Studies in History and Philosophy of Science Part A 36(1):43-60). There is also some related material in another notebook of the period ('Questiones quaedam philosophicae', 'Certain philosophical questions').
The 'Waste Book' seems to be the only Newton manuscript source offering advance hints of the third law before the 1684 manuscript 'De motu' (an initial precursor of 'Principia', written on the stimulus of questions put to Newton by Edmund Halley, and sent to Halley and to the Royal Society). The 'Waste Book' casts some light on the origins and justification of the third law, as discussed in the Fraser paper cited above (p.50): this mentions that while Newton's words suggest he thought it was obvious that action and reaction were opposite in direction, e.g. when two bodies press against each other, it was not so obvious at first that the action and reaction were also equal in size.
Much of the ingredient thinking on dynamics that went into the 'Waste Book' appears to have related to the problem of formulating laws that would account acceptably for the phenomena of bodies in collision. As also argued by Fraser (2005), some of the relevant arguments relate to the equal actions on bodies at both ends of a compressed spring.
All of these sources may give insight into Newton's thinking, but there remain always dangers of anachronism and misinterpretation in reading such documents; and on some points, the language of the sources can permit different authors to draw different conclusions about their content and implications. For example, R S Westfall (1971), 'Force in Newton's Physics' (at p.348) considering the Waste book, wrote that
"Except for the special case in which [two interacting bodies] p and r
have equal motions, the conclusion that they press each other equally
had seemed obviously false to the great majority of those who before
1665 had attempted to analyze the force of percussion. The Waste
book suggests that Newton came to deny the intuitively obvious by
recognising that for every impact, there is a frame of reference, that
of the common centre of gravity, in which the two bodies do have equal
forces. That is, his treatment of impact depended on his accepting a
relativity of motion in terms of which the idea of an absolute force
of a body's motion is meaningless."
On the other hand, Fraser (2005:53) thought that
"the evidence suggests that the third law originated in the empirical
or theoretical investigation of elasticity and that, for Newton, its
justification lay in his application of an elastic model of
collisions."
And then Westfall (1971:472) had already pointed out that
"in demonstrating the validity of the third law in the case of two
bodies attracting each other, Newton {for the sake of argument}
imagined B to attract A more strongly than A attracts B. If that
were the case, there would be an unbalanced force in the system
of two bodies, and the system would move in the line AB
‘in infinitum with a motion perpetually accelerated’ --
a situation contradicting the first law."
(with quote from the Scholium to the laws of motion (1729:p37)).
In this way numerous lines of argument converge on the third law. Whichever of them accounts better for the history of its development, the answer remains a 'yes', there are several antecedent hints or traces of the third law found in Newton's writing before the 'Principia' and before the 1684 'De motu', with clear signs that he gave attention to the subject matter in the 1660s.
As a postscript, it's also relevant that Newton made no claim that the laws of motion he stated in the 'Principia' were his own. In the 'Scholium' to the laws of motion Newton credited several others (Galileo, Wren, Wallis, Huygens, Mariotte). He also called the laws 'axioms', indicating that he thought they made generally acceptable starting-points not in need of proof: he wrote (1729 English translation of Principia, p.31) that they were "such principles as have been receiv'd by Mathematicians, and are confirm'd by abundance of experiments", i.e. largely experiments of others. (The naming of the laws as Newton's was made by others long after his lifetime: probably in recognition that as a set and a compilation they were not in use before Newton: he selected and combined them from among competing prior-proposed principles, and also amended their expression and scope. Concepts of action and reaction do predate Newton's work, but the third law gave precision to the concept of this paired interaction, e.g. R S Westfall (1971), 'Force in Newton's Physics': especially discussion of Newton's various drafts of laws of motion, pp.448-456.)
