There is no simple answer to your question, other than that far infrared diodes that I am aware of are relatively low power and will not heat anything much by radiative transfer.
For a slightly longer answer, your question breaks into several parts. First, long wave infrared is not a precisely defined term. It frequently means radiation with a wavelength from roughly 6 micrometers to roughly 14 micrometers, but other definitions exist.
Second, the transparency of materials varies widely, and often varies widely over this band. Materials which are relatively transparent a 6 micrometers may be totally opaque at 10 micrometers. You need to know the wavelength of the diode you propose using, and the specific material you propose for a window to answer your question. Many plastics are relatively transparent over parts or all of this band, but it varies with the specific mix of plastic. It is often easier to measure the transmission than to find the exact recipe of a piece of plastic and find transmission measurements made by someone else. Also relatively transparent does not mean 100%. 70% transmission would not be an unusual value. If you were to find a source which could do significant heating (10 W as an example), it would deposit significant heat (3 W in the example) in the window. This isn't necessarily a problem to the window, since you can arrange the beam size to be large as it goes through the window, resulting in low power density.
Third, the absorbtion of materials also varies widely with wavelength and surface treatment. You will again need to compare your sources wavelength with the proposed target. But a general comment is that the reason that metals get so hot sitting in the sun is that they are relatively good at absorbing the shorter wavelengths (.3 micrometers to 2 micrometers) that compose most of sunlight while they are poor radiators (which implies poor absorbtion) in the 6 micrometer to 14 micrometer wavelengths where room temperature objects radiate most of their heat. So your long wave source is unlikely to be an efficient heater of metal targets.