I figure this
Railroad Map of that time period would help in this discussion since you seem to like the Indianapolis option for reason that it was a rail hub at the time. I'm also including a map of major US
Water Courses because civil war era armies had to stay within close range of major watersheds in order to maintain position for more than a period of about three days which might be relevant later.
I think the best way to answer this question is to ask what the win conditions for the CSA were and how they might be effected. I see three scenarios that might have been possible had events played out differently as suggested.
1) The CSA snipes the federal capital and forces the federal government to concede to southern secession before the the CSA's meager military machine is burned out by attrition.
2) The CSA must somehow outlast the federals until the war loses political support due to public fatigue. The north had the resources to keep going practically indefinitely compared to the south if public support for the war persisted, but that was becoming a big problem by mid 1863 for Lincoln. This was a big reason why he promoted Grant to be the commander of all federal forces. Lincoln needed results and Grant had been the only general up to that point capable of delivering as demonstrated by the Vicksburg campaign.
3) Somehow, the federal government/military bungles things so badly that public support for the war evaporates much faster than it did in our timeline. This was definitely not out of the question considering the poor generalship of the AoP up until 1863. Basically, the north just walks away from the war and decides it's not worth their time anymore way ahead of schedule because of some horrific decision that leads to an overwhelming loss.
Now to answer your possibilities for alternate wartime capital locations if Maryland is now a part of the CSA:
Philadelphia) I think this is the most likely. It is well connected to rail and water ways, and really isn't in any worse of a position than D.C. had been in our timeline as concerns it's proximity to the CSA borders and seat of power. It also has the added benefit of allowing Lincoln to maintain the appearance of defending his greatest population centers (the ones that produce the vast majority of his public support, military manpower, and federal income). Also, losing Philly would be tantamount to losing the metaphorical heart of the nation because of the revolutionary history there. It would just be too great a blow to recover from. I don't think the union would have a choice but to aggressively defend it and the rest of the eastern seaboard behind it by extension, so why not make an intentional show of force out that defense instead?
New York) While it was the largest city in the union, withdrawing to New York to me displays a lack of faith in your ability to defend. As I explained above, I don't think the federals could have afforded themselves the option of withdrawing from the field further back than Philly without conceding the second or third CSA win conditions that I described earlier. There is no point in moving your capital to New York aside from putting distance between your head of state and the enemy, which would only slow crucial communication. By moving to new York, you could end up fully giving away all the advantages of the lower eastern seaboard while not picking up any exceptional benefits in return.
Indianapolis) This one is an interesting proposition, but I think it fails because (like New York) it jeopardizes Philly by obligating your primary defensive force to guard the governing apparatus which has now been far removed from the population it purports to be defending. Indy is well connected to transport infrastructure by that time, but it's still a good distance away from the industrial core of the union, again slowing the transmission of communication and supplies to the main force. I suppose you could still keep your primary force in the east, but then there's just no point at all to moving your capital so far away in the first place and doing so opens up CSA win condition option #1 if the south could manage to pull it off early. I don't think this would have been out of the question since Lee had a smaller and presumable more mobile army to maneuver into position than The federals. Add this to the fact that Scott, McClellan, and Halleck were all very cautious and defensively minded and I think you have a recipe for a quick southern victory by Lee that backdoor option.
So my answer out of the options you provided is Philadelphia. I could maybe see the government being moved to Harrisburg or York/Lancaster, PA but I think that's the furthest west that Lincoln might have dared to go. Defending Pennsylvania and especially Philadelphia would have been a win condition for Lincoln both militarily and politically. Losing both Baltimore and D.C. like you said would already have been a huge difficulty to overcome, but you can't give away the founding seat of the nation.
