Regime of unsteady flow over heat sink
Even if the flow was otherwise laminar, a square pin will have detached flow with a turbulent wake at anything but the slowest velocities. Where the laminar-turbulent transition occurs depends on the exact geometry, but roughness and sudden steps tend to promote turbulence. The flow through the duct ahead of the heat sink is also likely to be turbulent, being fast and most likely driven by a turbulence-producing fan. Don't place too much stock in the Reynolds number for determining if a flow is laminar, because once a flow becomes turbulent, it tends to stay turbulent. It's possible for the turbulence to dampen out, but usually that takes special design effort.

Having done both CFD simulations and simplified closed-form calculations of similar problems, I prefer closed-form. My approach would be to use the fin geometry and flow rate to calculate an equivalent film coefficient \$h\$ for a flat plate the same size as the base of the heat sink. Incropera and DeWitt's intro to heat transfer book is a good source for the formulas for that. Then use that as a boundary condition for conductive heat transfer from the dies to the heat sink surface. A steady-state heat conduction problem is much easier to set up, and faster to solve, than a transient CFD problem would ever be. At a minimum, it will be a good check against the simulation.