<Page>

                                                              Exhibit 99.906CERT

                            SECTION 906 CERTIFICATION

                Certification Pursuant to 18 U.S.C. Section 1350,
                             As Adopted Pursuant to
                  Section 906 of the Sarbanes-Oxley Act of 2002

Morgan Stanley New York Tax-Free Income Fund

     In connection with the Report on Form N-CSR (the "Report") of the
above-named issuer for the period ended December 31, 2005 that is accompanied by
this certification, the undersigned hereby certifies that:

1.   The Report fully complies with the requirements of Section 13(a) or 15(d)
     of the Securities Exchange Act of 1934; and

2.   The information contained in the Report fairly presents, in all material
     respects, the financial condition and results of operations of the Issuer.


Date: February 9, 2006                     /s/ Ronald E. Robison
                                           ---------------------
                                           Ronald E. Robison
                                           Principal Executive Officer


A signed original of this written statement required by Section 906 has been
provided to Morgan Stanley New York Tax-Free Income Fund and will be retained by
Morgan Stanley New York Tax-Free Income Fund and furnished to the Securities and
Exchange Commission or its staff upon request.

<Page>

                            SECTION 906 CERTIFICATION

                Certification Pursuant to 18 U.S.C. Section 1350,
                             As Adopted Pursuant to
                  Section 906 of the Sarbanes-Oxley Act of 2002

Morgan Stanley New York Tax-Free Income Fund

     In connection with the Report on Form N-CSR (the "Report") of the
above-named issuer for the period ended December 31, 2005 that is accompanied by
this certification, the undersigned hereby certifies that:

1.   The Report fully complies with the requirements of Section 13(a) or 15(d)
     of the Securities Exchange Act of 1934; and

2.   The information contained in the Report fairly presents, in all material
     respects, the financial condition and results of operations of the Issuer.


Date: February 9, 2006                    /s/ Francis Smith
                                          -----------------
                                          Francis Smith
                                          Principal Financial Officer


A signed original of this written statement required by Section 906 has been
provided to Morgan Stanley New York Tax-Free Income Fund and will be retained by
Morgan Stanley New York Tax-Free Income Fund and furnished to the Securities and
Exchange Commission or its staff upon request.