This is a difficult topic, because it's a very personal decision and there's no right answer. I myself got pregnant during my second year (surprise!) and had my son just before third year started. I was lucky to have understanding residents and attendings, particularly in the beginning who were flexible when I needed it. My husband, a law student, had a much more flexible schedule than I did, and we had a family member who did in-home daycare watch him during the first year. It took patience on my husbands part, and energy, but wasn't as hard as I thought. Well, missing my son was harder than I anticipated, but you'd see that in any profession, not just medicine.
Most women at my school opt to have kids at the very beginning of fourth year. This seems to work particularly well especially if you can get heavy fourth year rotations (sub-i's, etc) out of the way before the baby. Just remember to factor in time for both parts of Step 2 and residency interviews when figuring out vacation time. I've also known some people who've had kids in first and second year. If possible, try for the summer or a prolonged break period; I have a friend who had her baby during our first block of spring semester exams, and she ultimatley needed to take a semester off (best decision she could have made in the end).
My advice is to always plan for the unexpected. We all hope and pray for healthy babies, but unfortunately it isn't always the case. Or, you could have some unanticipated difficulties in your own recovery. Talk with your administration to make sure you'll have someone on your side and can make contingency plans. It's good to have people support you if you need to take a leave or something like that. Talk with your significant other and make sure they're ok with taking care of the baby by him/herself when you're on overnight call q4. Look into daycare programs asap. Remember to factor in studying for and taking boards and residency interviews. Talk with other women at your school who've had babies - they'll have good insight for you. Ultimately, you've got to figure out what works best for you, be ready to compromise and for the unexpected, but it's SO worth it.
PM with questions, happy to try and help.