I am going to respond to each question one at a time.
(1) In IPUMS USA, you can use the select cases tool when submitting your data extract. This allows you to only include cases matching a given set of characteristics (i.e., only in New York) in your data extract.
(2) I’m not exactly sure what you are referring to here when you say “using the SDA function.” In IPUMS USA (using either the data extract system or the online analysis tool—i.e., SDA) the lowest level of geographic identification available is the PUMA (public use microdata area). Therefore, census tracts are not identifiable in the public use microdata available via IPUMS USA. Aggregated data, at the census tract level, is available via the IPUMS NHGIS project. Regarding file format: Data from IPUMS USA can be downloaded in fixed width files with command files for Stata, SPSS, SAS, R, and can also be downloaded in .csv format. In IPUMS NHGIS, the data come in .csv format by default. In SDA, the online analysis tool does not currently support downloading tables, but you can copy and paste the contents of the entire table to an excel spreadsheet.
(3) Again, I’m not sure if you are referring to data from IPUMS USA or IPUMS NHGIS. It sounds like you are looking at a data file from IPUMS USA, but note that these data do not identify areas as small as census tracts. If you are using IPUMS USA, the command files will read in the necessary metadata so that your columns are labeled properly.