I'm a non-trad student. I supported my wife through medical school. Now she's out and supports me through medical school.
We had kid #1 between her M3 and M4 year, #2 between her PGY2 and PGY3 year, and #3 between my M1 and M2 year. So we've tried kids in preclinical years, clinical years, and residency.
Here's the scoop: it doesn't matter. One is not better than the other, and one is not worse than the other. Each has its own upsides and downsides.
The summer between M1/M2 is open so you won't have any conflicts or have to move/reschedule anything. Flipside is M3 year is likely to be a rude awakening for your spouse -- you start putting in doctors hours away from home. A toddler in that mix does add stress.
Between M3/M4 was pretty convenient, too. She basically deferred starting M4 for a while and then came back to a research block followed by a path block -- i.e., easy hours. Flipside is residency interviews are coming up and you'll be traveling a bit, finishing up your Step 2s, and preparing to move.
PGY2/PGY3 was hardest simply because of the demanding schedule, but she ended up just taking FMLA and extending her residency by a few months.