I know this is fairly late but I'll give you an answer.

To begin, and to be as brief as possible, the IRA had a simple structure in itself but it's relation to its political wing, Sinn Féin isn't as simple. To dumb it down a lot the Party and Army are both a part of what's typically called 'The Republican Movement', essentially one's job was to advance it politically and with propaganda while the other would do it through force of arms, neither had full seniority over the other in theory but in practice the Army typically dominated the Party until the mid 80s when they became more even and the mid 90s when the Party became dominant.

Now, comes the difficult part, The Army would meet at a 'General Army Convention' to debate policy, define a constitution and elect a 12 member executive who's job it was to select a 7 man 'Army Council' who would run the Army on a day to day basis and elect a 'Chief of Staff' from their own ranks (or appoint someone else in very rare cases) who in turn would select an 'Adjutant General' (second in command, like a VP) and establish a 'General Headquarters' which would include officers to head departments such as engineering, arms and importantly for this publicity.

Now if you're thinking this sounds similar-ish to a politcal party you'd be right as an IRA GAC and Sinn Féin Ard Féis were very similar in process. But here's the thing, while the Army Council was elected by the Army it had control over both the Army and the Party, this stems from the 1916 proclamation of the Republic which stipulated that an Army Council would control Ireland until it could elect its own government (with some key requirements such as women had to be allowed to vote for it to be deemed legitimate). As the AC ruled over both sides then both members of the IRA and SF could and have sat on the AC, although it should be noted that membership often overlapped between the Party and Army.

Now taking what we know then the President of the Party was subservient to the AC and existed in the same frame as the Army leadership, by this count Margaret Buckley who was the president of SF from 1937 to 1950 could be viewed as the most senior female leader within the 'Republican Movement, especially as she was instrumental in repairing the links between the IRA and SF.

Now! (that's 4 nows if you're counting) The IRA and SF were not always the only two members of the RM as they were joined by the Cumann na mBan and the Fianna Éireann, a women's wing and a youth wing respectively. These two groups were absorbed by the IRA during the 1969-98 conflict but if we could say until that absorbtion then the leader of CmB was the highest ranking woman. However from this point you get Constance Markievicz who lead both the FÉ and CmB at various points while also commanding troops during the Easter rising and being extremely influential in the Irish Citizen Army could be counted as the highest ranking woman in the movement ever.

And now we get to perhaps the most complicated and unsatisfying viewpoint.

Ok, so I've operated in this answer assuming that when you said IRA that you meant the whole continuity of IRA history but now I'm going to look at the 1969-98 period which I'm assuming you actually meant. The (Provisional) IRA began with quite a conservative opinion on women, their rights, place in society and capacity in combat roles but eventually came to accept women as equals as the campaign continued. This means that women didn't ever gain a position on the AC or become the CoS but did become OCs or Officer Commanding. An OC was the member that ran a unit whether that be an ASU or a group of prisoners in a prison and as many of the Female IRA members ended up in Armagh Women's Jail they had their own OCs. Further more women became quite prominent bomb builders(an important position) such as current MEP Martina Anderson who at the time of her arrest became one of only two female Category A prisoners in England(The other also being a female IRA member).

Further on this we simply don't know, mixed gender units did exist but who was in charge wasn't always defined and some individual women shot to prominence like Spy Rosena Brown who became daubed the IRA Mata Hari but didn't have any special rank. But here's the real kicker there were no ranks in the (P)IRA for its members in practice, if a member was killed regardless of position held they would all be listed as Volunteer/Óglach meaning that women held the highest rank while only ever holding mid tier positions.

Hope this helps.