Best method for measuring very young plant growth?
I am assuming you want to monitor these traits in controlled conditions because in wild type conditions it will be real challenge to monitor in details unless you have easily accessible way (like leave surface area and related visual traits). Remember these techniques will change according to your plant/seed and your study interest. Lot of things change during development. You need to look at characters which suits your study. You can try following, 


Monitor real time oxygen consumption in controlled chamber ( Generally researcher do this by monitoring loss of oxygen in
current chamber by some non invasive method. However there are
other techniques like this which can be also implemented
depending on type of plant.)
There are some automated image acquisition techniques like this or this
Use of volatile organic compound (VOCs) traces 
Change is fresh and dry weight during development
Root moisture sensors ( in microgravity environment ) like this
I don't know whether you can use this kind of sensors in any way but these are very useful in monitoring particular element in vivo


This is very big list. There many other components which you can monitor like protein content, lipids etc. However such techniques are most reliable but destructive and you can use if you have large amount of samples.   You can go through papers cited in above list. Take a look at their methods and materials. You will know how to do such measurements and what are advantages/disadvantages.