Broke it down in a little more detail (with the extra info about Infestation just provided by Bobby)
Feudal Japan
Flashbacks from Secret History #1-4, TMNT MS #5 and TMNT #5
Early 2010
May 2010
Events of 18 months ago (TMNT #1)
August 2010
Events of 15 months ago (TMNT #1-4)
December 2010
Leonardo, Donatello and Michelangelo are given their weapons (TMNT #5)
November 2011
Teenage Mutant Ninja Turtles #1 - Change is Constant Part 1
Teenage Mutant Ninja Turtles #2 - Change is Constant Part 2
Teenage Mutant Ninja Turtles #3 - Change is Constant Part 3
Teenage Mutant Ninja Turtles #4 - Change is Constant Part 4
December 2011
Teenage Mutant Ninja Turtles #5 - Enemies Old, Enemies New (Prologue)
Teenage Mutant Ninja Turtles Micro-Series #1 - Raphael
Teenage Mutant Ninja Turtles Micro-Series #2 - Michelangelo
Early January 2012
Teenage Mutant Ninja Turtles #6 - Enemies Old, Enemies New Part 1
Hero Comics 2012 - Ready Set Go!
Teenage Mutant Ninja Turtles Mirco-Series #3 - Donatello
Infestation 2 #1
Infestation 2: Teenage Mutant Ninja Turtles #1
Infestation 2: Teenage Mutant Ninja Turtles #2
Infestation 2 #2
Teenage Mutant Ninja Turtles #7 - Enemies Old, Enemies New Part 2
Teenage Mutant Ninja Turtles #8 - Enemies Old, Enemies New Part 3
Teenage Mutant Ninja Turtles Micro-Series #4 - Leonardo
Teenage Mutant Ninja Turtles #9 - Shadows of the Past Part 1
Teenage Mutant Ninja Turtles #10 - Shadows of the Past Part 2
Teenage Mutant Ninja Turtles #11 - Shadows of the Past Part 3
Teenage Mutant Ninja Turtles Micro-Series #5 - Splinter (set during TMNT #11)
Teenage Mutant Ninja Turtles #12 - Shadows of the Past Part 4
Mid/Late January 2012 - Original Chronological Order
Teenage Mutant Ninja Turtles Micro-Series #7 - April
Teenage Mutant Ninja Turtles Micro-Series #6 - Casey Jones
Teenage Mutant Ninja Turtles #13 - Sins of the Fathers Part 1
Teenage Mutant Ninja Turtles #14 - Sins of the Fathers Part 2
Teenage Mutant Ninja Turtles Micro-Series #8 - Fugitoid
Teenage Mutant Ninja Turtles Annual 2012
Teenage Mutant Ninja Turtles #15 - Blood Brothers Part 1
Teenage Mutant Ninja Turtles #16 - Blood Brothers Part 2
Mid/Late January 2012 - Revised Reading Order (no affect to chronology)
Teenage Mutant Ninja Turtles Micro-Series #6 - Casey Jones
Teenage Mutant Ninja Turtles #13 - Sins of the Fathers Part 1
Teenage Mutant Ninja Turtles #14 - Sins of the Fathers Part 2
Teenage Mutant Ninja Turtles Micro-Series #7 - April
Teenage Mutant Ninja Turtles Annual 2012
Teenage Mutant Ninja Turtles #15 - Blood Brothers Part 1
Teenage Mutant Ninja Turtles #16 - Blood Brothers Part 2
Teenage Mutant Ninja Turtles Micro-Series #8 - Fugitoid
February 2012
Teenage Mutant Ninja Turtles #17 - Krang War Part 1
Teenage Mutant Ninja Turtles #18 - Krang War Part 2
Teenage Mutant Ninja Turtles #19 - Krang War Part 3
Teenage Mutant Ninja Turtles #20 - Krang War Part 4
Teenage Mutant Ninja Turtles Micro-Series Villains #1 - Krang
March/April 2012 (Approx)
Secret History of the Foot Clan #1-4
Teenage Mutant Ninja Turtles #21 - City Fall (Prologue)
Teenage Mutant Ninja Turtles Micro-Series Villains #2 - Baxter Stockman (thematic placement is after Krang, release/chronological here)
Teenage Mutant Ninja Turtles Micro-Series Villains #4 - Alopex
Teenage Mutant Ninja Turtles #22 - City Fall Part 1
Teenage Mutant Ninja Turtles #23 - City Fall Part 2
Teenage Mutant Ninja Turtles Micro-Series Villains #3 - Old Hob (set during TMNT #23)
Teenage Mutant Ninja Turtles #24 - City Fall Part 3
Teenage Mutant Ninja Turtles Micro-Series Villains #5 - Karai
Teenage Mutant Ninja Turtles #25 - City Fall Part 4
May 2012 (Approx)
Teenage Mutant Ninja Turtles Micro-Series Villains #6 - Hun
Teenage Mutant Ninja Turtles #26 - City Fall Part 5
Teenage Mutant Ninja Turtles Micro-Series Villains #7 - Bebop & Rocksteady
Teenage Mutant Ninja Turtles #27 - City Fall Part 6
Teenage Mutant Ninja Turtles #28 - City Fall Part 7
Teenage Mutant Ninja Turtles Micro-Series Villains #8 - Shredder
UPCOMING
Teenage Mutant Ninja Turtles #29 - Northampton Part 1
Teenage Mutant Ninja Turtles #30 - Northampton Part 2
Teenage Mutant Ninja Turtles #31 - Northampton Part 3
Teenage Mutant Ninja Turtles #32 - Northampton Part 4
Utrom Empire #1-3
The 2 orders for the events of mid/late January are due to a new, approved reading order by Editor Bobby Curnow. According to original editor's notes the April micro took place before the Casey micro and discussion at the time placed the Fugitoid micro in release order after #14. With hindsight Bobby has agreed that the story flows better if the micros are read before their respective thematic arc. There are no chronological problems with either order.