The answer to this question depends very much on how you view both poems and the concerns that Milton expresses within them. Arguably, both offer a strong thematic unity in what Milton hopes to achieve through them, but it is clear after even a cursory reading that both poems are very different and have different purposes. In "On the Morning of Christ's Nativity," for example, it is clear that Milton has a cosmic vision as he seeks to offer a vision of the complete spiritual and religious significance of Christ's birth:
Say, Heavenly Muse, shall not thy sacred vein
Afford a present to the Infant God?
Hast thou no verse, no hymn, or solemn strain,
To welcome him to this his new abode...
The scope and purpose of this poem is very different as Milton seeks to explore in this panegyric the full significance of the Incarnation and to reflect on how it impacted world history and also the very spiritual bedrock of life.
"Lycidas," by contrast, is ostensibly a personal lament for one of Milton's friends. However, it is clear that the death of Milton's friend is used by him to raise certain issues and attack certain attitudes prevalent during his life and times. This is particularly evident when the allegory of the poem and the parallel between the shepherds and their flock and the church and their congregations is established. Note how the speaker criticises the "shepherds" and their preference for personal gain over the spiritual health of their "flock":
Of other care they little reck'ning make,
Then how to scramble at the shearers feast,
And shove away the worthy bidden guest.
Blind mouthes! that scarce themselves know how to hold
A Sheep-hook, or have learn'd ought els the least
That to the faithfull Herdmans art belongs!
Note how the speaker presents the leaders of the church as being only interested in their own health and as being completely unfit to be shepherds, as they "scarce themselves know how to hold/A Sheep-hook." This poem therefore clearly is rooted in the present and is used by Milton to attack certain issues of relevance to his day, and arguably issues that are still important.
Both poems therefore are very different in terms of their scope and purpose, and because of this it is difficult to state whether one or the other offers a better synthesis of theme. "On the Morning of Christ's Nativity" is an early work of Milton, and as such "Lycidas" is arguably better crafted, but apart from this the poems are very different and are difficult to compare in the way suggested by this question.