Although I am not involved in aquaculture (my current research involves greenhouse gas emissions from dairy cattle farming), I am interested in knowing how other food products contribute to global greenhouse gas emissions. In that sense your question is very interesting.
According to the IPCC 5th assessment report (which can be found here:
http://www.ipcc.ch/report/ar5/wg3/
(please see: Chapter 11, Box 11.4 in page 834 of the report), global N2O emissions from aquaculture in 2009 were estimated to be 43 Mt CO2eq, and will increase to 178 Mt CO2eq by 2030, which could account for 5.7 % of global anthropogenic N2O emissions (if aquaculture continues to grow at the present growth rate of about 7.1 % / yr).
IPCC report does not provide the total GHG emissions or ‘carbon footprint’ of global aquaculture; however, the following FAO report provides a wealth of information related to this topic.
Link to FAO report:
http://www.fao.org/docrep/017/i3062e/i3062e.pdf
Especially, please see page 94 (presentation by P. Tyedmers) of the report, you may find it useful.