For Sivir using Chalice would it be better to use flat +mana or mana/5 glyphs?
Which is better for a strong early/mid game and why?

Mana/5 and get them per level.

Even with full mana seals (flat or per level), that's less than two extra boomerang tosses. After five minutes, if you're past level four, the per level mana regen seals will give back more mana than you get added from the mana seals (flat or per level). And not only do they get even better with each level, but Chalice of Harmony makes them more effective.

I know from experience that with full mana regen per level seals and chalice of harmony you can spam Boomerang Blade and keep Ricochet up. They're way more useful than a little extra max mana.

The easiest way to tell (for any flat versus /level ones) is to divide the total the flat is giving you by the amount the per level one gives you. This tells you how long before the per level version provides more. Example:

Yellow
Greater Seal of Replenishment = .41 mana regen / 5
divided by
Greater Seal of Clarity = .1 mana regen / 5 per level

= 4.1

You have to round it up to 5, but basically you will have the same regen from the two Seals by the time you reach level 5. Then you get to make a choice based upon your mana consumption as to whether you need the extra .2 mana regen / 5 for the first couple of levels.

I think you should go with the per level runes for mana regen, and possibly you may be able to ditch your Chalice completely if you can manage your mana better. Depends on the character and how much you burn skills.

If you are in a solo lane and you get all the exp from the dying creeps (not being forced to BP or run out of range) you will be level 5 shortly after the 5 minute mark. Roughly 3 minutes of actual combat where the flat mana regen are better.